Bioconductor Packages

Analysis of Alternative Splicing Using RNA-Seq

BBCAnalyzer: an R/Bioconductor package for visualizing base counts

Forge your own BSgenome data package

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

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

Efficient manipulation of biological strings

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

End-to-End Analysis of Small RNA-Seq Data from Viroids

Tools for curating, analyzing, and manipulating biological sequences

DiffLogo: A comparative visualisation of biooligomer motifs

Identification and Annotation of Protein Hotspot Residues

FFPE Artificial Chimeric Read Filter for NGS data

Compute the automorphisms between DNA's Abelian group representations

Representation and manipulation of short genomic alignments

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Guitar

Interlog protein network reconstruction by Mapping and Mining ANalysis

Intron-Exon Retention Estimator

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Analyze high-throughput sequencing of T and B cell receptors

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

Perform Methylation Analysis on Next Generation Sequencing Data

Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

Open Reading Frames in Genomics

OUTRIDER - OUTlier in RNA-Seq fInDER

Quasispecies Diversity

Quantify and Annotate Short Reads in R

An R package for RNA visualization and analysis

RFGeneRank: Cross-validated Stable Predictive Gene Ranking for Transcriptomics

R bowtie wrapper

An R Wrapper for Bowtie2 and AdapterRemoval

An R Wrapper for nvBowtie and nvBWT, a rewritten version of Bowtie2 for cuda

R wrapper for BWA-backtrack and BWA-MEM aligners

Bioinformatics pipelines based on Rcwl

R Wrapper for HISAT2 Aligner

Differential pattern analysis for Ribo-seq data

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

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

Mapping, quantification and variant analysis of sequencing data

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

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

NGS Read Simulator for FFPE Tissue

An R package to identify functional impacts due to alternative RNA processing events

Implementation of the dot bracket annotations with Biostrings

Software Package for Transcription Factor Binding Site (TFBS) Analysis

TVTB: The VCF Tool Box

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

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

Automated analysis of CRISPR experiments