Biocview "ImmunoOncology"

A/B compartment inference from ATAC-seq and methylation array data

Accurate, high-resolution sample inference from amplicon sequencing data

A collection of tools for imaging MS data processing

A correlation-based method for quality filtering of single-cell RNAseq data

Add-on to CellNOptR: Discretized time treatments

Add-on to DESeq to improve p-values and q-values

A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes

A Framework for Quality Control

A GAM based framework for analysis of ChIP-Seq data

A GatingML Interface for Cross Platform Cytometry Data Sharing

AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype

A mass spectrometry imaging toolbox for statistical analysis

A model for network-based prioritisation of genes

Analysis and quantitation of isobarically tagged MSMS proteomics data

Analysis for short time-series data

Analysis of Alternative Splicing Using RNA-Seq

Analysis of cell-based screens - revised version of cellHTS

Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Analysis Of Differential Abundance Taking Sample Variation Into Account

Analysis of high-throughput microscopy-based screens

Analysis of Metabolomics GC/MS Data

Analysis Tools for 10X V(D)J Data

Analytical R tools for Mass Spectrometry

Analytical Tools for MassArray Data

Analyze flow cytometric data using gate information

Analyze flow cytometric data using histogram information

Analyze Illumina Infinium DNA methylation arrays

Analyze isomiRs and miRNAs from small RNA-seq

Analyze thermal proteome profiling (TPP) experiments

Analyze Transcription Factor Enrichment

An Easy-to-use Systematic pipeline for ATACseq data analysis

An effective identification of alternative splicing events using junction arrays and RNA-Seq data

An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification

An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps

An interface between R and MS-GF+

An interface package for the BIOM file format

An mzIdentML parser for R

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

Annotation and analysis of biological dynamical systems using flow cytometry

A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

An package for identification of novel peptides by customized database derived from RNA-Seq

An R interface for computational modeling of tumor progression

An R interface to the Common Workflow Language

An R interface to the Ontology Lookup Service

An R package for flow data clustering

An R package for gene and isoform differential expression analysis of RNA-seq data

An R package for prediction of nucleosome positions

An R package for proteomics data quality control

An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

An R package for the Bayesian analysis of differential subcellular localisation experiments

An R package for the creation of complex genomic profile plots

An R Package for Unbiased Splicing Pathway Analysis

An R package to detect chromatin state switches from epigenomic data

A package for the analysis of GC-MS metabolite profiling data

A package for variant peptides detection and visualization in shotgun proteomics.

A package to run mixture models for truncated metabolomics data with normal or lognormal distributions

Approximate posterior estimation for GLM coefficients

ArrayExpress High Throughput Sequencing Processing Pipeline

A search tool for single cell RNA-seq data by gene lists

A shiny GUI for MSGFplus

A small RNA-seq visualizer and analysis toolkit

Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

Assess Differential Gene Expression Experiments with ERCC Controls

Assessment of duplication rates in RNA-Seq datasets

Assign Properties to TNBC Patients

A suite of functions to facilitate zFPKM transformations

ATAC-seq Quality Control

A Tool for Generic Cell Type Enrichment Analysis

A tool for unsupervised projection of single cell RNA-seq data

A toolkit for performing KNN-based statistics for flow and mass cytometry data

A toolkit for single-cell immune receptor profiling

a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

A tool to use GO Subtrees to Tag and Annotate Genes within a set

A unifying bioinformatics framework for spatial proteomics

Automated analysis of CRISPR experiments

Automated Optimization of XCMS Data Processing parameters

Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations

Automatic and interactive quality control for flow cytometry data

Baffling Recursive Algorithm for Isotope distributioN calculations

Base Functions and Classes for Mass Spectrometry and Proteomics

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Batch Effects Quality Control Software

Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments

Bayesian ANalysis Of Compositional Covariance

Bayesian Analysis of Differential Expression in RNA Sequencing Data

Bayesian Analysis of Single-Cell Sequencing data

Bayesian clustering and imputationa of single cell methylomes

Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations

Bayesian modelling of cell-to-cell DNA methylation heterogeneity

BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)

BEAT - BS-Seq Epimutation Analysis Toolkit

Better prediction by use of co-data: Adaptive group-regularized ridge regression

Bias Awared Peak Calling and Quantification for MeRIP-Seq

Bias-free Footprint Enrichment Test

Binomial test for Hi-C data analysis

Bioconductor components for general cancer genomics

Bioinformatics pipelines based on Rcwl

Biological Network Analysis

Breakpoint analysis of time-course expression data

Bump Hunter

Calculate growth-rate inhibition (GR) metrics

Calculate strandness information of a bam file

Cancer Clone Finder

Causal network analysis methods

ccrepe_and_nc.score

Cell OrderiNg by FluorEScence Signal

CellRanger Input/Output

CEllular Latent Dirichlet Allocation

Characterization of Alternative Splicing based on Paired-End Reads

ChIP-Seq data scaling according to spike-in control

chroGPS2: Generation, visualization and differential analysis of epigenome maps

Chromatin Variation Across Regions

C++ infrastructure for representing and interacting with the gated cytometry data

Ciphergen SELDI-TOF Processing

Clonogenic Survival Analysis in R made easy!

Clustering Algorithms for Bioconductor

Clustering and Resolution Enhancement of Spatial Transcriptomes

Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models

Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Clustering for Flow Cytometry

Clustering of Time Series Gene Expression data

Cluster Merging for Flow Cytometry Data

Codon Usage Analysis and Prediction of Gene Expressivity

Co-Expression Analysis of Sequencing Data

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Co-expression Modules identification Tool

Collection of annotation related methods for mass spectrometry data

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Combinatorial Polyfunctionality Analysis of Single Cells

Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

Combining multitube flow cytometry data by binning

Compare Characteristic Features of Count Data Sets

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Computational pipeline for computing probability of modification from structure probing experiment data

Computes estimates of the probability of related individuals sharing a rare variant

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Conditional quantile normalization

Condition Comparison in scRNA-seq Data

Context-Aware Transcript Quantification from Long Read RNA-Seq data

Controlling bias and inflation in association studies using the empirical null distribution

Coordinate Covariation Analysis

Coordinated Gene Activity in Pattern Sets

CopyKit

Copy number calling and SNV classification using targeted short read sequencing

Copy number information from targeted sequencing using off-target reads

Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments

cosmiq - COmbining Single Masses Into Quantities

Count summarization and normalization for RNA-Seq data

Covariate Assisted Large-scale Multiple testing

Coverage visualization package for R

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Create rapid visualizations of RNAseq data in R

Cross omic genetic fingerprinting

Cross-target analysis of small molecule bioactivity

Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

Cytometry dATa anALYSis Tools

Data analysis for cell-based functional assays

Data and code resources for microsatellite instability studies

Data extraction pipeline for large-scale GC-MS metabolomics datasets

Data Mining for RNA-seq data: normalization, feature selection and classification

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

Decomposition of Isotopic Patterns

Deconvolution of mixed cells from spatial and/or bulk gene expression data

DeepBlueR

DegNorm: degradation normalization for RNA-seq data

derfinder helper package

Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)

Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

Determination of essential phenotypic elements of clusters in high-dimensional entities

DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates

Differential abundance analysis with a right censored covariate in high-dimensional cytometry

Differential Abundant Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data

Differential Co-expression Analysis

Differential discovery in high-dimensional cytometry via high-resolution clustering

Differential Enrichment analysis of Proteomics data

Differential Enrichment Scan 2

Differential expression analysis and model fitting for single-cell RNA-seq data

Differential Expression Analysis for RNA-seq data through a robust variance component test

Differential expression analysis of longitudinal count data sets

Differential expression using kernel-based score test

Differential gene expression analysis based on the negative binomial distribution

Differential gene expression data formats converter

Differential gene usage in immune repertoires

Differentially Expressed Gene-Gene pairs

Differential pattern analysis for Ribo-seq data

Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

Discriminant Analysis for Evolutionary Inference

Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles

ELBOW - Evaluating foLd change By the lOgit Way

Empirical Analysis of Digital Gene Expression Data in R

Empirical Bayes estimate of block diagonal covariance matrices

Empirical RNA-seq Sample Size Analysis

Engineering Evaluation by Gene Categorization (eegc)

Ensemble of Gene Set Enrichment Analyses

Epigenetic Dissection of Intra-Sample-Heterogeneity

Estimate Pairwise Interactions from multidimensional features

Estimate proliferation in cell-tracking dye studies

Estimate protein complex membership using AP-MS protein data

Estimate Systems Immune Response from RNA-seq data

ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition

Experimental Design in Differential Abundance analysis

Exploration of marker-gene sequence taxonomic annotations

Exploratory analysis and differential expression for RNA-seq data

Exploratory Data Analysis and Normalization for RNA-Seq

Exploratory Data Analysis of LC-MS/MS data by spectral counts

Explore and download data from the recount project

Exposome and omic data associatin and integration analysis

Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data

Fast Correlation Based Filter for Feature Selection

Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

FCBF-based Co-Expression Networks for Single Cells

Filter replicated high-throughput transcriptome sequencing data

Finding differentially expressed unannotated genomic regions from RNA-seq data

Find Specificity Groups with GLIPH and GLIPH2 Method

Fitting cell population growth models

Flexible, isoform-level differential expression analysis

flowBeads: Analysis of flow bead data

flowClean

flowCore: Basic structures for flow cytometry data

flowPlots: analysis plots and data class for gated flow cytometry data

FlowRepository R Interface

Functions to conduct quality control analysis in methylation data

GaGa hierarchical model for high-throughput data analysis

GC-SIM-MS data processing and alaysis tool

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Gene Ontology analyser for RNA-seq and other length biased data

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data

Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

Generating SAM file for PSMs in shotgun proteomics data

Generating Tree Hierarchy Visualizations from Gene Expression Data

Gene set analysis following differential expression using linear (mixed) modeling with dream

Gene Set Enrichment Analysis Extended to Contingency Cubes

Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Gene Set Enrichment For ChIP-seq Peak Data

Gene Set Enrichment / Projection Displays

Gene set over-representation, enrichment and network analyses for high-throughput screens

Gene-Specific Phenotype EstimatoR

GenoMetric Query Language for R/Bioconductor

Genomic trajectories with heterogeneous genetic and environmental backgrounds

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Graphical User Interface for IsoCorrectoR

GUIDE-seq analysis pipeline

GUIDE-seq and PEtag-seq analysis pipeline

Handling and analysis of high-throughput microbiome census data

HDF5 backend for DelayedArray objects

HDF5 datasets as array-like objects in R

Hexbin plots for single cell omics data

Hierarchical Gating Pipeline for flow cytometry data

Hits Selection for Synthetic Lethal RNAi Screen Data

HLA typing clustering and visualization based on specific similarity metrics

iASeq: integrating multiple sequencing datasets for detecting allele-specific events

Identification of cancer cell lines based on their weighted mutational/ variational fingerprint

Identification of candidate causal perturbations from differential gene expression data

Identification of genetic Variants affecting Alternative Splicing

Identifies cell population in flow cytometry data.

Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Identify Contaminants in Marker-gene and Metagenomics Sequencing Data

Identify Differentially Expressed Genes from RNA-seq data

Identifying differential cell populations in flow cytometry data accounting for marker frequency

Identify likely duplicate samples from genomic or meta-data

immune Cell Analysis Tool

immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay"

Import and summarize transcript-level estimates for transcript- and gene-level analysis

Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

Improves Early Build Genome Assemblies using Strand-Seq Data

Imputation-guided re-construction of complete methylomes from WGBS data

Independent Hypothesis Weighting

Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure

Inference of differential exon usage in RNA-Seq

Inferring metabolic networks from untargeted high-resolution mass spectrometry data

Infers biological signatures from gene expression data

Infers clonal composition of a tumor

Infrastructure for representing and interacting with gated and ungated cytometry data sets.

InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

Integrated Copy Number Variation detection

Integrating Cap Enrichment with Transcript Expression Analysis

Integrative analysis of Multi-omics data for Alternative Splicing

Integrative Statistics of alleLe Dependent Expression

Interactive Analysis of Single Cell RNA-Seq Data

Interactive Cytometry Gating in R

Interactive Differential Expresion Analysis Browser

Interactive Differential Expression AnaLysis

Interactive SummarizedExperiment Explorer

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package

Interactive Visualization of RNA-seq Data Using a Principal Components Approach

Interfaces the tandem protein identification algorithm in R

Interface to the RDP Classifier

Intron-Exon Retention Estimator

Investigation of Fragmentation Conditions in Top-Down Proteomics

iSEE Universe

Iteratively Adjusted Surrogate Variable Analysis

JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

L1-regularization based methods for detection of differential splicing

Label-free data analysis pipeline for optimal identification and quantitation

LC-MS and GC-MS Data Analysis

LC-MS/MS Differential Expression Tests

Linear model and normality based normalization and transformation method (Linnorm)

Linear Models for Microarray Data

Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

LoomExperiment container

Machine Learning Interface for RNA-Seq Data

MACS: Model-based Analysis for ChIP-Seq

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

Make read coverage plots from BigWig files

Manipulate Zarr archives as R objects

Manipulating and exploring protein and proteomics data

Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test

Mapping, quantification and variant analysis of sequencing data

Marker Gene Finder in RNA-seq data

Massive correlating biclusters for gene expression data and associated methods

Mass spectrum processing by wavelet-based algorithms

Matching and meta-clustering in flow cytometry

Maximum Likelihood Decay Modeling of RNA Degradation Data

Meta-analysis for the metagenomic read counts data from different cohorts

Meta-analysis of RNA-Seq count data in multiple studies

Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.

MetaCyto: A package for meta-analysis of cytometry data

Methods for imaging mass cytometry data analysis

Methods for Single-Cell RNA-Seq Data Analysis

Methods for TCR single-cell embedding

Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

Methylated CpGs Set Enrichment Analysis

Methylation-Based Inference of Regulatory Activity

Microbial Assemblage Normalized Transcript Analysis

Microbiome Exploration App

MiRNA Ranking by Gene Expression

Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

Mixture Models for Single-Cell Assays

Model higher-order methylation profiles

Monte Carlo Reference-based Consensus Clustering

MS-based metabolomics annotation pipeline

msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions

Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform

Multilevel Model for Multivariate Responses with Missing Values

Multi-Modal Single-Cell Analysis Methods

Multi-sample multi-group scRNA-seq data analysis tools

Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.

Negative Binomial Models to detect Differential Splicing

NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing

Non-parametric Flow Cytometry Data Gating

Normalization of single cell RNA-seq data

ODE add-on to CellNOptR

Omics Data Integration Project

One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)

ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics

Open Reading Frames in Genomics

Open-source toolkit to analyse data from xCELLigence System (RTCA)

Optimal p-value weighting with independent information

Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq

Outlier-aware and Count-based Compositional Analysis of Single-cell Data.

OUTRIDER - OUTlier in RNA-Seq fInDER

PAIRADISE: Paired analysis of differential isoform expression

Parameter Optimization for Flow Cytometry Data Transformation

parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)

parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)

Parsing pepXML files and filter based on peptide FDR.

PathoStat Statistical Microbiome Analysis Package

PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

Peak Detection for Mass Spectrometry data using wavelet-based algorithms

Perform a maximum contrast projection of 3D images along the z-dimension into 2D

Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data

PharmacOGenomics Ontology Support

Phenotyping Flow Cytometry Assays

Phylogenetic partitioning based ILR transform for metagenomics data

Pipeline for single cell multi-omic data pre-processing

pipeline for single cell RNA-seq data analysis

Plotting functions for derfinder

Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Power Estimation Tool for RNA-Seq and proteomics data

Precict cis-co-accessibility from single-cell chromatin accessibility data

Predict cis-co-accessibility from single-cell chromatin accessibility data

Prediction of gestational age with Illumina HumanMethylation450 data

Prediction of pri-miRNA Transcription Start Site

Predict metabolic pathway activity based on metabolomics data

Prize: an R package for prioritization estimation based on analytic hierarchy process

Probe region expression estimation for RNA-seq data for improved microarray comparability

Projection-based Gating Strategy Optimization for Flow and Mass Cytometry

PROspective Power Evaluation for RNAseq

Protein Micro Array Data Management and Interactive Visualization

Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Provides a GUI for DAPAR

Provides a GUI for rTANDEM

Publication-ready volcano plots with enhanced colouring and labeling

Quality control and analysis tools for Illumina DNA methylation BeadChip

Quality Control for Single-Cell RNA-seq Data

Quality Control of Gated Flow Cytometry Experiments

Quantification and Visualization of Variations of Splicing in Population

Quantification and Visulization of Variations of Splicing in Population

Quantification of the Tumor Immune contexture from RNA-seq data

Quantify and Annotate Short Reads in R

Quantify and interpret divers of variation in multilevel gene expression experiments

Quantify and interpret drivers of variation in multilevel gene expression experiments

qusage: Quantitative Set Analysis for Gene Expression

Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

Reconstruction, visualization and analysis of branching trajectories

Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

Regression Models with Multivariate Outcomes for Mass Cytometry Experiments

Remove Unwanted Variation from RNA-Seq Data

Report of DEG analysis

Representation and manipulation of short genomic alignments

Reproducibility-Optimized Test Statistic

Reproducible GSEA Benchmarking

Reusable and reproducible Data Management

R Interface to the metaviz web app for interactive metagenomics data analysis and visualization

R Interface to the ProteomeXchange Repository

RNA-seq data analysis using the Poisson-Tweedie family of distributions

RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

RnaSeqSampleSize

rnaSeq secondary analyses

RnBeads

Robust prediction of clinical outcomes using cytometry data without cell gating

Robust statistical inference for quantitative LC-MS proteomics

R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

S4 Classes for Single Cell Data

S4 Class for Spatial Experiments handling

S4 Class for Spatially Resolved -omics Data

samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation

Sample Classifier

Sample size for RNAseq studies

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

scDataviz: single cell dataviz and downstream analyses

Seamless navigation through combined results of set-based and network-based enrichment analysis

Search for correlation between epigenetic signals and gene expression in TADs

Semantic labelling of flow cytometric cell populations

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

Shiny app GUI wrapper for ggplot with built-in statistical analysis

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

SigFuge

Significance-based Modules Integrating the Transcriptome and Epigenome

Similarity measures for chemical compounds

Simple Simulation of Single-cell RNA Sequencing Data

Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Simulation, power evaluation, and sample size recommendation for single cell RNA-seq

Single-Cell Analysis Toolkit for Gene Expression Data in R

Single-Cell Consensus Clustering

Single Cell Differential Expression

Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)

Single Cell Overview of Normalized Expression data

Single cell replicability analysis

Single-Cell RNA-Seq Analysis Utilities

Single-cell RNA sequencing data normalization

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)

Sparse Data Observations for Simulating Synthetic Abundance

Spatial Image Analysis of Tissues

Splice event prediction and quantification from RNA-seq data

Splice Interpreter of Transcripts

Stability Ranking

Standardize Antibody Names

Stan implementation of BASiCS

Statistical analysis for sparse high-throughput sequencing

Statistical analysis for the Colony Formation Assay

Statistical Analysis of High-Throughput Genetic Perturbation Screens

Statistical analysis of high-throughput RNAi screens

Statistical Analysis of Metabolomic Data

Statistical Analysis of Molecular Profiles

Statistical Analysis of MPRA data

Statistical analysis of sequins

Statistical Characterization of Post-translational Modifications

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site

Statistical methods for the analysis of flow cytometry data

Statistical tools and data structures for plate-based flow cytometry

Statistics and dIagnostic Graphs for HTS

Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Subsampling of high-throughput sequencing count data

Suite of Functions for Pooled Crispr Screen QC and Analysis

Surrogate Variable Analysis

SVAPLSseq-An R package to estimate the hidden factors of unwanted variability and adjust for them to enable a more powerful and accurate differential expression analysis based on RNAseq data

Switch-like differential expression across single-cell trajectories

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: Workflow Environment for Data Analysis and Report Generation

Targeted Learning with Moderated Statistics for Biomarker Discovery

TCC: Differential expression analysis for tag count data with robust normalization strategies

T-cell Receptor/Immunoglobulin Profiler (TRIP)

Test for differential expression for RNA-seq data

The Cancer Genome Atlas Data Integration

The Discordant Method: A Novel Approach for Differential Correlation

The Genomic STate ANnotation Package

Time-Course Multi-Omics data integration

Tools for counting and visualising mutations in a target location

Tools for curating, analyzing, and manipulating biological sequences

Tools for high-throughput metabolomics

Tools for making reports in various formats

Tools for processing of high-dimensional cytometry data

Tools for qPLEX-RIME data analysis

Tools for quantitative proteomics data analysis

Tools for spliced gene structure manipulation and analysis

Tools for working with diverse immune genes

Topology-based pathway analysis of RNA-seq data

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Transcript expression inference and differential expression analysis for RNA-seq data

Transcriptional analysis based on transcriptograms

Transcript Quantification Import with Automatic Metadata

Transform and Filter SWATH Data for Statistical Packages

tricycle: Transferable Representation and Inference of cell cycle

TRONCO, an R package for TRanslational ONCOlogy

uORF prediction in R

Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression

Using Mass Cytometry for Differential Abundance Analyses

uSORT: A self-refining ordering pipeline for gene selection

Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Utilities for flow cytometry

Utilities for Handling Single-Cell Droplet Data

Variance stabilization in flow cytometry (and microarrays)

Visual and interactive gene expression analysis

Visual Exploration of Omic Datasets Using a Shiny App

Visualise microarray and RNAseq data using gene ontology annotations

Visualization for flow cytometry

Visualization of highly multiplexed imaging data in R

Visualization of multi-dimentional cancer genomics data

Visualize Cytometry data with ggplot

Workflow to process tandem MS files and build MassBank records

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Biocview "ImmunoOncology"

R Package Documentation

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