Packages
98 packages on Bioconductor tagged Spatial or GeneRegulation or ChIPSeq, most distinct IPs first
Spatial, GeneRegulation and ChIPSeq in Topics
| Package | Maintainer | Category | Latest version | Distinct IPs a month | Needs |
|---|---|---|---|---|---|
| edgeR Empirical Analysis of Digital Gene Expression Data in RYunshun Chen | Yunshun Chen | software | 19 Oct 2026 | 32,392 | 10 |
| DESeq2 Differential gene expression analysis based on the negative binomial distributionMichael Love | Michael Love | software | 28 Apr 2026 | 32,072 | 54 |
| TCGAbiolinks TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC dataTiago Chedraoui Silva | Tiago Chedraoui Silva | software | 28 Apr 2026 | 6,750 | 103 |
| TFBSTools Software Package for Transcription Factor Binding Site (TFBS) AnalysisGe Tan | Ge Tan | software | 28 Apr 2026 | 4,721 | 79 |
| ChIPseeker ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationGuangchuang Yu | Guangchuang Yu | software | 28 Apr 2026 | 3,962 | 158 |
| regioneR Association analysis of genomic regions based on permutation testsBernat Gel | Bernat Gel | software | 28 Apr 2026 | 2,952 | 64 |
| Rsubread Mapping, quantification and variant analysis of sequencing dataWei Shi | Wei Shi | software | 28 Apr 2026 | 2,951 | 8 |
| CNEr CNE Detection and VisualizationBoris Lenhard | Boris Lenhard | software | 28 Apr 2026 | 2,692 | 112 |
| ALDEx2 Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor | Greg Gloor | software | 28 Apr 2026 | 2,533 | 56 |
| systemPipeR systemPipeR: A Multipurpose Workflow Management System for Reproducible Data AnalysisThomas Girke | Thomas Girke | software | 28 Apr 2026 | 2,506 | 94 |
| DiffBind Differential Binding Analysis of ChIP-Seq Peak DataRory Stark | Rory Stark | software | 21 Jul 2026 | 2,490 | 141 |
| viper Virtual Inference of Protein-activity by Enriched Regulon analysisMariano J Alvarez | Mariano J Alvarez | software | 28 Apr 2026 | 2,060 | 87 |
| GreyListChIP Grey Lists -- Mask Artefact Regions Based on ChIP InputsMatt Eldridge | Matt Eldridge | software | 28 Apr 2026 | 1,942 | 59 |
| ChIPpeakAnno Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval dataJianhong Ou | Jianhong Ou | software | 10 Aug 2026 | 1,898 | 125 |
| motifStack Plot stacked logos for single or multiple DNA, RNA and amino acid sequenceJianhong Ou | Jianhong Ou | software | 28 Apr 2026 | 1,782 | 111 |
| chipseq chipseq: A package for analyzing chipseq dataBioconductor Package Maintainer | Bioconductor Package Maintainer | software | 28 Apr 2026 | 1,626 | 54 |
| QuasR Quantify and Annotate Short Reads in RMichael Stadler | Michael Stadler | software | 28 Apr 2026 | 1,551 | 114 |
| csaw ChIP-Seq Analysis with WindowsAaron Lun | Aaron Lun | software | 28 Apr 2026 | 1,536 | 46 |
| derfinder Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approachLeonardo Collado-Torres | Leonardo Collado-Torres | software | 28 Apr 2026 | 1,535 | 137 |
| qpgraph Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics DataRobert Castelo | Robert Castelo | software | 28 Apr 2026 | 1,495 | 81 |
| GUIDEseq GUIDE-seq and PEtag-seq analysis pipelineLihua Julie Zhu | Lihua Julie Zhu | software | 28 Apr 2026 | 1,256 | 179 |
| ChIPQC Quality metrics for ChIPseq dataTom Carroll | Tom Carroll | software | 19 May 2026 | 1,221 | 159 |
| INSPEcT Modeling RNA synthesis, processing and degradation with RNA-seq dataStefano de Pretis | Stefano de Pretis | software | 28 Apr 2026 | 1,213 | 123 |
| nucleR Nucleosome positioning package for RAlba Sala | Alba Sala | software | 28 Apr 2026 | 1,145 | 76 |
| BCRANK Predicting binding site consensus from ranked DNA sequencesAdam Ameur | Adam Ameur | software | 28 Apr 2026 | 1,138 | 15 |
| rTRM Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction NetworksDiego Diez | Diego Diez | software | 28 Apr 2026 | 1,117 | 47 |
| recoup An R package for the creation of complex genomic profile plotsPanagiotis Moulos | Panagiotis Moulos | software | 28 Apr 2026 | 1,098 | 119 |
| MEDIPS DNA IP-seq data analysisLukas Chavez | Lukas Chavez | software | 28 Apr 2026 | 1,093 | 102 |
| pandaR PANDA AlgorithmJoseph N. Paulson | Joseph N. Paulson | software | 28 Apr 2026 | 1,093 | 37 |
| Linnorm Linear model and normality based normalization and transformation method (Linnorm)Shun Hang Yip | Shun Hang Yip | software | 28 Apr 2026 | 1,088 | 62 |