Biocview "DataImport"

Accelerated similarity searching of small molecules

Access HDF5 content from h5serv

Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

A compilation of ENCODE metadata

A compilation of metadata from NCBI SRA and tools

A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)

Add resources to ExperimentHub

A DownStream Chemo-Proteomics Analysis Pipeline

Affymetrix File Parsing SDK

A GatingML Interface for Cross Platform Cytometry Data Sharing

A generic R plugin dispatcher for BASE

A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops

Algorithms and data structures for large single-cell expression matrices

Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Analysis of Agilent Microarray Data [draft]

Analysis of alternative poly A site usage

Analysis of Brain Imaging Data

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Analysis of Illumina microarray data [A DRAFT - TRUE]

Analysis of Large Affymetrix Microarray Data Sets

Analysis of Single-Cell CRISPR Screen Data

Analytical Tools for MassArray Data

Analyze Illumina Infinium DNA methylation arrays

An interface package for the BIOM file format

An mzIdentML parser for R

Annotate the Gene Symbols for Probes in Expression Array

Annotation and analysis of biological dynamical systems using flow cytometry

Annotation and gene expression data retrieval from Bgee database

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

Annotation of Genetic Variants

A normalization and copy number estimation method for single-cell DNA sequencing

An R interface to the Rfam database

An R Object-oriented Microarray Analysis package

An R package facilitating analysis of RNA modifications, structures, and interactions

An R package for RNA visualization and analysis

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 the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

an R package for visualization of tree and annotation data

An R Package to Collect Everyones Homework

An R toolkit for non-coding RNA

'Antares' Results Processing

A package for importing and analyzing data from Roche's Genome Sequencer System

A package to search and retrieve data from Hub resources

API access to Ocean Genomics txome.ai RNA-seq Analysis

A pipeline for processing drug sensitivity screen data

A Pipeline to Process RNAseq Data

A probe-level data file format used by aroma.affymetrix [DEPRECATED]

A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]

A Simple Data Management and Sharing Tool

A Thin Wrapper around the ImmuneSpace Data and Tools Portal

A Thin Wrapper around the ImmuneSpace Database

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

A toolkit for APA analysis using RNA-seq data

A tool set for 3D Trans-Omic network visualization with Cytoscape

A Tool to Analyze and Design NGS Based Custom Gene Panels

Augmented functionality for analysis of epigenomic variance

Automated analysis of high-throughput qPCR data

Automated spectraL Processing System for NMR

Automatic Statistical Identification in Complex Spectra

A work flow for analysis and normalization of pre-processing RT-qPCR data

A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Base Classes and Functions for Phylogenetic Tree Input and Output

Base Functions and Classes for Mass Spectrometry and Proteomics

Base NanoString Experiment Class

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

Big multivariate data plotted interactively

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

Binding site defintion based on iCLIP data

Bioconductor Algorithms for Big Data

Bioconductor Management with Portable Encapsulated Project (PEP) Objects

biodb, a library and a development framework for connecting to chemical and biological databases

biodbChebi, a library for connecting to the ChEBI Database

biodbExpasy, a library for connecting to Expasy ENZYME database.

biodbHmdb, a library for connecting to the HMDB Database

biodbKegg, a library for connecting to the KEGG Database

biodbLipidmaps, a library for connecting to the Lipidmaps Structure database

biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database

biodbUniprot, a library for connecting to the Uniprot Database

Bioinformatics pipelines based on Rcwl

Broadcast data between R and Gaggle

Browse the Human Cell Atlas data portal

Building Expression Atlas from RNA-Seq data

Cache files downloaded from S3

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

CDF Environment Maker

Cell OrderiNg by FluorEScence Signal

CellRanger Input/Output

CEllular Latent Dirichlet Allocation

CGH Micro-Array NORmalization

Cheminformatics Toolkit for R

ChIPanalyser: Predicting Transcription Factor Binding Sites

chipseq: A package for analyzing chipseq data

ChIP-Seq data scaling according to spike-in control

ChIPUtils - A package to perform exploratory analysis of ChIP data and most commonly used QC measures

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

Classes and functions for Array Comparative Genomic Hybridization data

Classes and Methods for Handling Genomic Interaction Data

Client to access AnnotationHub resources

Client to access ExperimentHub resources

Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

Cluster and Tree Conversion.

Clustering and Resolution Enhancement of Spatial Transcriptomes

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

CMap Tools in R

CNE Detection and Visualization

co-expressed gene-set enrichment analysis

Competitive Balances for Taxonomic Enrichment Analysis in R

Compiling Bioconductor to Handle Each Matrix Type

Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Compute cell-type specific enrichments with high resolution

Compute coverage matrices from recount quickly using bwtool

Connect high throughput Array data from different platforms

Convenience Functions for Biscuit

Convenience package for solving some liftover challenges

Conversion Between scRNA-seq Objects

Converting experimental metadata from ISA-tab into Bioconductor data structures

Convert the GatingSet from Boost serialization to protocol buffer format

CopyKit

Copy-Number Analysis of Large Microarray Data Sets

Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

COVID-19 data resources and analysis tools

Create and Manager a Database specifically for Bioconductor build report statuses

Create Copy-Number Plots using karyoploteR functionality

Cross-target analysis of small molecule bioactivity

Cytometry dATa anALYSis Tools

Data Independent Acquisition Library Editing to Convert The Species

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

Data resource for package "TRESS"

DeepBlueR

DegNorm: degradation normalization for RNA-seq data

Detection of de novo deletion in targeted sequencing trios

Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)

Detection of subclonal SNVs in deep sequencing data.

Differential pattern analysis for Ribo-seq data

Distributed computing by file or by range

Downloads ENA Fastqs With GEO Accessions

Easy Use R

Efficient algorithms for DNA methylation

Efficient compression and analysis of Hi-C Data

Efficient manipulation of biological strings

Enabling stream processing of large files

Estimates Isoform Specific RPF Footprint Densities

Explore and download data from the recount3 project

Explore and download data from the recount project

Exposome exploration and outcome data analysis

Extraction of Differential Gene Expression

Extract read count signals from bam files

Fast full-text and DNA search in NCBI RefSeq, UniProt-KB and genome sequence

FASTQ input and manipulation

Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files

Fast treatment of MACSQuantify FACS data

FDR-controlled analysis of 2D-TPP experiments with replicates

FDR-controlled analysis of SPP experiments

File-System Toolbox for RAVE Project

Find SNV/Indel differences between two bam files with near relationship

Fitting cell population growth models

Framework for Storing and Accessing Hi-C Data Through HDF Files

Functionality to Read and Manipulate SomaLogic ADAT files

Functionality Visualization for Motifs

Functions used to preprocess datasets stored in BioDataome

Further Utilities for Genomic Interactions

GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays

GEM: fast association study for the interplay of Gene, Environment and Methylation

GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens

Gene Expression Atlas query and gene set enrichment package.

Gene Haplotype Statistics, Phenotype Association and Visualization

Generate and Manipulate Genomic Ranges

Generating Tree Hierarchy Visualizations from Gene Expression Data

Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

GeneRegionScan

Generic and Biological Sequences

Gene transfer format files for common ChIP-seq model organisms

GenoMetric Query Language for R/Bioconductor

Get data from NCBI Gene Expression Omnibus (GEO)

gQTLBase: infrastructure for eQTL, mQTL and similar studies

GUI for limma Package with Affymetrix Microarrays

GUI for limma Package With Two Color Microarrays

Guitar

GWAS trait-associated SNP enrichment analyses in genomic intervals

HDF5 backend for DelayedArray objects

HDF5 Compression Filters

HDF5 datasets as array-like objects in R

HDF5 Delayed Array for Nifti Objects

Hexbin plots for single cell omics data

Hierarchical Gating Pipeline for flow cytometry data

High throughput prioritized acquisition and processing of tandem mass spectra

High-Throughput Sequence Analysis using the Aroma Framework

htslib high-throughput sequencing library as an R package

HTSlib high-throughput sequencing library as an R package

Human ChIP-seq peaks data from ENCODE and ROADMAP Epigenomics

Human Protein Atlas in R

Identifies false positives of CNV calling tools by using SNV calls

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

Identifying differential DNA loops from chromatin topology data

Illumina methylation array analysis for large experiments

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

immune Cell Analysis Tool

Implementation of the dot bracket annotations with Biostrings

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

Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

Importing a tRNAscan-SE result file as GRanges object

Importing from tRNAdb and mitotRNAdb as GRanges objects

Import, Manipulate and Explore the Results of an 'Antares' Simulation

Import methods for 10X Genomics files

Import, Modify, and Export Motifs with R

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

Infrastructure for Mass Spectrometry Experiments

Infrastructure for microfluidic oscillatory washing-based ChIP

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

Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

Interaction Based Homogeneity for Evaluating Gene Lists

Interactive Cytometry Gating in R

Interface for the Reactome Content Service

Interface for the Reactome Graph Database

Interface to the RDP Classifier

Interval-Wise Testing for Omics Data

Introduce *Ranges to bedtools users

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Large-scale single-cell RNA-seq data manipulation with GDS files

Linear Models for Microarray Data

Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

LoomExperiment container

LowMACA - Low frequency Mutation Analysis via Consensus Alignment

m6Aexpress-BHM: Predicting m6A regulation of gene expression in multiple-groups context by a Bayesian Hierarchical Mixture model

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

Manage Files Across Sessions

Manages subsets of data with Bioconductor Experiment objects

Manipulate Zarr archives as R objects

Manipulating and exploring protein and proteomics data

Manipulation of Codelink microarray data

Marker Enrichment Modeling (MEM)

Mass spectrometry Data Backend for Bruker TimsTOF Files

Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files

Mass Spectrometry Data Backend for MassBank record Files

Mass Spectrometry Data Backend for NIST msp Files

megadepth: BigWig and BAM related utilities

Methods for accessing online The Cancer Genome Atlas (TCGA) data

Methods for Continuous Flow Cytometry

Methods for identifying small RNA loci from high-throughput sequencing data

Methods for imaging mass cytometry data analysis

Methods for reading CNAG files

Methods for reading dChip files

Methods for Reading dChip Files

Methylation array and sequencing spatial analysis methods

Microarray Analysis of Differential Expression

Microarray and RNA-seq Processing for ImmuneSpace

Microbial Assemblage Normalized Transcript Analysis

Microbiome analysis

Mining, Calling, and Importing Epigenomic Peaks in R

Mismatch Tolerant Maximum Common Substructure Searching

Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

motif matching, comparison, and de novo discovery using the MEME Suite

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

Multiple Sample Peak Calling

Multiple Sequence Alignment with MUSCLE

Multivariate Analysis of Genotype–Phenotype Association and Visualization for 3D Image

NanoString GeoMx Tools

NanoString nCounter Tools

NDEx R client library

Network Analysis for Omics Data

NEUral network-based single-Cell Annotation tool

NGS Read Simulator for FFPE Tissue

NIH / NCI Genomic Data Commons Access

Normalization and difference calling in ChIP-seq data

Normalization and reporting of Illumina SNP bead arrays

Nucleosome positioning package for R

OmniPath web service client

OmniPath web service client and more

OnASSIs Ontology Annotation and Semantic SImilarity software

OpenAccess TCGA Data on Terra as MultiAssayExperiment

Open Reading Frames in Genomics

Operations on genomic intervals

Optimising the Definition of Expressed Regions

Optimized Functional Annotation Of ChIP-seq Data

Optimized LC-MS Spectra Processing

Out-of-core statistical computing and signal processing

Package for CTDbase data query, visualization and downstream analysis

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)

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

Parsing GenBank files into semantically useful objects

Parsing Illumina Microarray Output Files

Peptide correlation analysis

Perform Methylation Analysis on Next Generation Sequencing Data

Pipeline for single cell multi-omic data pre-processing

Plot customizable linear genomes displaying arbitrary data

Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

Position-Dependent Kernel Association Test

Predicting context-specific m6A regulation of gene expression

Predicting context-specific m6A regulation of gene expression combinding m6A reader binding information

Pre-process 1H-NMR FID signals

Preprocessing tools for oligonucleotide arrays

Preprocessing tools for oligonucleotide arrays.

Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Processing of adductomic mass spectral datasets

Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Proteomics Standard Initiative Common QUery InterfaCe

protrusionproteome

Provides access to pathogen annotation resources available on EuPathDB databases

Provides structure and functions for the analysis of OTU data

psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders

Putting the fun in LINCS L1000 data analysis

QA/QC of a gVCF or VCF file

qiime2R

Quality Assessment Tools for Oxford Nanopore MinION data

Quality control and analysis tools for Illumina DNA methylation BeadChip

Quality Control of Protemics Data

Quality Control Tool for High-Throughput Sequencing Data

Quantitative comparison of multiple ChIP-seq datasets

Quasispecies Diversity

query gene expression data and plots from BrainStars (B*)

Quick Read Quality Control

R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts

R Client for GA4GH API

R Client for Google Genomics API

R Client for Seven Bridges Genomics API (v1)

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

Read qPCR data

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

Reorganization of rhdf5client code

Repetitive Element Methylation Prediction

Representation and manipulation of short genomic alignments

Retrotransposed transcript detection from structural variants

Reusable and reproducible Data Management

R framework for exploration and analysis of respirometry data

RiboseQC, a Comprehensive Ribo-Seq Analysis Tool

RImmPort: Enabling Ready-for-analysis Immunology Research Data

R Interface for the Basic Local Alignment Search Tool

R interface to a subset of OpenBabel functionalities

R interface to Bio-Formats

R Interface to CoreArray Genomic Data Structure (GDS) Files

R interface to EBI MGnify metagenomics resource

R interface to genome annotation files and the UCSC genome browser

R Interface to HDF5

R Interface to the ProteomeXchange Repository

R Investigation of ChIP-chip Oligoarrays

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

RNA-Seq Utilities

RnBeads

Routines for the functional analysis of biological networks

Routines that don't belong to the core flow packages yet.

R package implementing the Cytoscape Exchange (CX) format

R Packages for Gene Haplotype Analysis

R SDK for BaseSpace RESTful API

rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers

R-side access to published microbial signatures from BugSigDB

R wrapper for Progenetix

S4 Classes for Single Cell Data

S4 Class for Spatial Experiments handling

S4 Class for Spatially Resolved -omics Data

Save Delayed Operations to a HDF5 File

Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data

scDataviz: single cell dataviz and downstream analyses

Segvis: A package for visualization of high throughput sequencing data along genomic segments

Serialization for MultiAssayExperiment Objects

Set of tools to identify periodic occurrences of k-mers in DNA sequences

Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

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

Similarity measures for chemical compounds

Simple tiling array analysis of Affymetrix ChIP-chip data

Single-cell analysis toolkit for gene expression data in R

Single-Cell Analysis Toolkit for Gene Expression Data in R

Single-Cell RNA-Seq Analysis Utilities

Single-Cell RNA-Seq Utilities

Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

Software set for alignment of biological replicate data

Spatial Image Analysis of Tissues

Spatial Overlay for Omic Data from Nanostring GeoMx Data

Spatial Transcriptomics Analysis

SpotClean adjusts for spot swapping in spatial transcriptomics data

spsBio: A systemPipeShiny plugin for biological data visualization

SQL-based Mass Spectrometry Data Backend

Sscore2: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays

Standard Input and Output for Bioconductor Packages

Statistical Analysis of the GeneChip

Statistical Utility for RBP (RNA binding protein) Functions

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: Workflow Environment for Data Analysis and Report Generation

systemPipeShiny: An Interactive Framework for Workflow Management and Visualization

TARgeted SEQuencing Experiment Quality Control

TCGA utility functions for data management

Test branch renaming

Test Single Package Builder

The BRENDA Enzyme Database

The Cancer Genome Atlas Data Integration

Thermal proximity co-aggregation with R

Tidy Meta Profiles using Bioconductor and the Tidyverse

Tool for Evaluation of Cell Identity from Transcription Profiles

Tools for analysing methylation patterns at genomic tuples

Tools for computing, querying and storing linkage-disequilibrium data

Tools for curating, analyzing, and manipulating biological sequences

Tools for data visualization

Tools for HELP data analysis

Tools for masking out problematic Affymetrix probes using VCF files and the oligo package

Tools for parsing Affymetrix data files

Tools for processing of high-dimensional cytometry data

Tools for qPLEX-RIME data analysis

Tools for quantitative proteomics data analysis

tools for spike-in UMI analysis

Tools for the Differential Analysis of Proteins Abundance with R

Tools for the Efficient Analysis of High-Resolution Genomics Data

Tools for Working With Synteny Objects

Track Cells, Analyze Cell Trajectories and Compute Migration Statistics

Transcriptome-guided quality assessment of m6A-seq data

Transcript Quantification Import with Automatic Metadata

Transform public data resources into Bioconductor Data Structures

Transform public proteomics data resources into Bioconductor Data Structures

TRONCO, an R package for TRanslational ONCOlogy

TSS sequencing data analysis

Turn Bioconductor objects into tidy data frames

TVTB: The VCF Tool Box

Unified statistal Modeling of Omics Data

uORF prediction in R

User Friendly Single-Cell and Bulk RNA Sequencing Visualization

Utilities for handling genomic interaction data

Utilities for Handling Single-Cell Droplet Data

Utilities to create and use Bioconductor Hubs

Variant annotations for structural variants

Very simple high level analysis of Affymetrix data

Visualise methylation data from Oxford Nanopore sequencing

Visualization and annotation of read signal over genomic ranges with profileplyr

Visualization of highly multiplexed imaging data in R

Visualization of Phylogenetic Networks

Working with Illumina Basecalling and Demultiplexing input and output files

Working with modified nucleotide sequences

You Only Lookup One (small part of an otherwise large matrix)

Biocview "DataImport"

R Package Documentation

Browse R Packages

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