Biocview "Alignment"

A graphical interface for the metagene package

Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection

Analysis of alternative splicing using RNA-Seq

Analysis of Alternative Splicing Using RNA-Seq

Analyze high-throughput sequencing of T and B cell receptors

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

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

An R interface to the GMAP/GSNAP/GSTRUCT suite

An R package for RNA visualization and analysis

An R package for the creation of complex genomic profile plots

an R package for visualization of tree and annotation data

An R Wrapper for Bowtie2 and AdapterRemoval

A package to produce metagene plots

Automated analysis of CRISPR experiments

BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

Base Classes and Functions for Phylogenetic Tree Input and Output

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

BBCAnalyzer: an R/Bioconductor package for visualizing base counts

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

Bioinformatics pipelines based on Rcwl

Building Expression Atlas from RNA-Seq data

Calculate strandness information of a bam file

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

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

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

Compares the genetic/epigenetic features between cancer cell lines with different dependencies of a gene set (signature)

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Conditional reciprocal best hits (CRBHits) in R

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

Cut rDNA Sequences Into Domains Using Covariance Models

DegNorm: degradation normalization for RNA-seq data

Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Detection of site fixation in molecular evolution

Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output

Differential Analyis of Hi-C Data

Differential pattern analysis for Ribo-seq data

DiffLogo: A comparative visualisation of biooligomer motifs

distSTRING calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

Dynamic Programming Based Alignment of MS2 Chromatograms

EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices

Efficient manipulation of biological strings

Extract read count signals from bam files

Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

FFPE Artificial Chimeric Read Filter for NGS data

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

Functionality Visualization for Motifs

Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences

Generate synthetic nucleosome maps

Gimpute: An efficient genetic data processing and imputation pipeline

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Guitar

GWAS trait-associated SNP enrichment analyses in genomic intervals

Identification and Annotation of Protein Hotspot Residues

Identification of putative mammalian orthologs to given enhancer

Implementation of the dot bracket annotations with Biostrings

Interactive Analysis of Single Cell RNA-Seq Data

Interface for Popular Multiple Sequence Alignment Tools

Interface to Call Programs from Infernal RNA Covariance Model Package

Interface to the RDP Classifier

Interlog protein network reconstruction by Mapping and Mining ANalysis

Intron-Exon Retention Estimator

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Lineage tracing by indels

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

Mapping, quantification and variant analysis of sequencing data

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

Methylation Analysis Based on Signal Detection

MethylIT utility

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

Multiple Sequence Alignment

Multiple Sequence Alignment Handling and Inspection

Multiple Sequence Alignment with MUSCLE

NGS Read Simulator for FFPE Tissue

Normalization and difference calling in ChIP-seq data

Open Reading Frames in Genomics

Outlier detection in multiple sequence alignments

OUTRIDER - OUTlier in RNA-Seq fInDER

Perform Methylation Analysis on Next Generation Sequencing Data

Perform Needleman-Wunsch algorithm

Phylogeny-based sequence clustering with site polymorphism

Plot Multiple Sequence Alignment using 'ggplot2'

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

Predicting context-specific m6A regulation of gene expression

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

Prediction of Protein Conserved Regions Using NADDA Algorithm

Pre-processing PTR-TOF-MS Data

Quantify and Annotate Short Reads in R

Quasispecies Diversity

Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

R bowtie wrapper

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

Representation and manipulation of short genomic alignments

Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation

R Interface for the Basic Local Alignment Search Tool

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

R Wrapper for HISAT2 Aligner

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

sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

scanMiR

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

SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

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

Set of tools to make V-plots and compute footprint profiles

SIMD Partial Order Alignment in R

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Software Package for Transcription Factor Binding Site (TFBS) Analysis

Software set for alignment of biological replicate data

Statistical Utility for RBP (RNA binding protein) Functions

Synteny Alignment and Analysis for Saccharomyces sensu stricto

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: Workflow Environment for Data Analysis and Report Generation

TARgeted SEQuencing Experiment Quality Control

Tools for curating, analyzing, and manipulating biological sequences

Transcriptome CUTteR

Transcriptome-guided quality assessment of m6A-seq data

Translational control assessment from ribosome footprint and total RNA libraries

TSS sequencing data analysis

TVTB: The VCF Tool Box

UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

uORF prediction in R

Visualization of Phylogenetic Networks

Visualization Tool for Genetic Reassortment

Visualization Tool for Sequence Recombination and Reassortment

Visualization tools for gene fusions

What the package does (short line)

Biocview "Alignment"

R Package Documentation

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