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Topic: Spatial or GeneRegulation or Transcriptomics

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Release: Release 3.4 (2016)

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69 packages on Bioconductor tagged Spatial or GeneRegulation or Transcriptomics, most distinct IPs first

Spatial, GeneRegulation and Transcriptomics in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
limma
Linear Models for Microarray and Omics DataGordon Smyth		Gordon Smythsoftware10 Aug 202645,9656
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202632,39210
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202612,63578
scran
Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202610,13962
TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC dataTiago Chedraoui Silva		Tiago Chedraoui Silvasoftware28 Apr 20266,750103
tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysisMichael Love		Michael Lovesoftware28 Apr 20265,8043
TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) AnalysisGe Tan		Ge Tansoftware28 Apr 20264,72179
MAST
Model-based Analysis of Single Cell TranscriptomicsAndrew McDavid		Andrew McDavidsoftware28 Apr 20263,74056
topGO
Enrichment Analysis for Gene OntologyFederico Marini		Federico Marinisoftware28 Apr 20263,22848
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20263,21199
ropls
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics dataEtienne A. Thevenot		Etienne A. Thevenotsoftware28 Apr 20262,96997
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
CNEr
CNE Detection and VisualizationBoris Lenhard		Boris Lenhardsoftware28 Apr 20262,692112
ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor		Greg Gloorsoftware28 Apr 20262,53356
DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataRory Stark		Rory Starksoftware21 Jul 20262,490141
viper
Virtual Inference of Protein-activity by Enriched Regulon analysisMariano J Alvarez		Mariano J Alvarezsoftware28 Apr 20262,06087
qpgraph
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics DataRobert Castelo		Robert Castelosoftware28 Apr 20261,49581
SC3
Single-Cell Consensus ClusteringVladimir Kiselev		Vladimir Kiselevsoftware28 Apr 20261,36892
made4
Multivariate analysis of microarray data using ADE4Aedin Culhane		Aedin Culhanesoftware28 Apr 20261,27938
GUIDEseq
GUIDE-seq and PEtag-seq analysis pipelineLihua Julie Zhu		Lihua Julie Zhusoftware28 Apr 20261,256179
INSPEcT
Modeling RNA synthesis, processing and degradation with RNA-seq dataStefano de Pretis		Stefano de Pretissoftware28 Apr 20261,213123
BCRANK
Predicting binding site consensus from ranked DNA sequencesAdam Ameur		Adam Ameursoftware28 Apr 20261,13815
rTRM
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction NetworksDiego Diez		Diego Diezsoftware28 Apr 20261,11747
pandaR
PANDA AlgorithmJoseph N. Paulson		Joseph N. Paulsonsoftware28 Apr 20261,09337
psichomics
Graphical Interface for Alternative Splicing Quantification, Analysis and VisualisationNuno Saraiva-Agostinho		Nuno Saraiva-Agostinhosoftware31 May 20261,070205
MoonlightR
Identify oncogenes and tumor suppressor genes from omics dataMatteo Tiberti		Matteo Tibertisoftware28 Apr 20261,048186
LOLA
Locus overlap analysis for enrichment of genomic rangesNathan Sheffield		Nathan Sheffieldsoftware28 Apr 20261,03924
pqsfinder
Identification of potential quadruplex forming sequencesJiri Hon		Jiri Honsoftware28 Apr 20261,02818
RTN
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulonsMauro Castro		Mauro Castrosoftware28 Apr 20261,023142
triplex
Search and visualize intramolecular triplex-forming sequences in DNAJiri Hon		Jiri Honsoftware28 Apr 20261,02217