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Topic: Transcription or ExpressionData

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Release: Release 3.15 (2022)

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243 packages on Bioconductor tagged Transcription or ExpressionData, most distinct IPs first

Transcription and ExpressionData 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
DESeq2
Differential gene expression analysis based on the negative binomial distributionMichael Love		Michael Lovesoftware28 Apr 202632,07254
EnhancedVolcano
Publication-ready volcano plots with enhanced colouring and labelingJared Andrews		Jared Andrewssoftware28 Apr 20267,62025
tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysisMichael Love		Michael Lovesoftware28 Apr 20265,8043
celldex
Index of Reference Cell Type DatasetsAaron Lun		Aaron Lunexperiment5 May 20265,71795
TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) AnalysisGe Tan		Ge Tansoftware28 Apr 20264,72179
AUCell
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)Gert Hulselmans		Gert Hulselmanssoftware29 Apr 20264,610115
decoupleR
decoupleR: Ensemble of computational methods to infer biological activities from omics dataPau Badia-i-Mompel		Pau Badia-i-Mompelsoftware30 Oct 20253,63441
tximeta
Transcript Quantification Import with Automatic MetadataMichael Love		Michael Lovesoftware26 Oct 20262,485108
goseq
Gene Ontology analyser for RNA-seq and other length biased dataFederico Marini		Federico Marinisoftware28 Apr 20262,404104
scRNAseq
Collection of Public Single-Cell RNA-Seq DatasetsAaron Lun		Aaron Lunexperiment5 May 20262,314121
PCAtools
PCAtools: Everything Principal Components AnalysisJared Andrews		Jared Andrewssoftware28 Apr 20261,88965
quantiseqr
Quantification of the Tumor Immune contexture from RNA-seq dataFederico Marini		Federico Marinisoftware28 Apr 20261,72758
RcisTarget
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regionsGert Hulselmans		Gert Hulselmanssoftwareno date on record1,724
qpgraph
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics DataRobert Castelo		Robert Castelosoftware28 Apr 20261,49581
IsoformSwitchAnalyzeR
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq dataKristoffer Vitting-Seerup		Kristoffer Vitting-Seerupsoftware28 Apr 20261,421151
SC3
Single-Cell Consensus ClusteringVladimir Kiselev		Vladimir Kiselevsoftware28 Apr 20261,36892
fishpond
Fishpond: downstream methods and tools for expression dataMichael Love		Michael Lovesoftware28 Apr 20261,36354
scmap
A tool for unsupervised projection of single cell RNA-seq dataVladimir Kiselev		Vladimir Kiselevsoftware28 Apr 20261,27062
iSEE
Interactive SummarizedExperiment ExplorerKevin Rue-Albrecht		Kevin Rue-Albrechtsoftware28 Apr 20261,237109
SGSeq
Splice event prediction and quantification from RNA-seq dataLeonard Goldstein		Leonard Goldsteinsoftware28 Apr 20261,22780
affylmGUI
GUI for limma Package with Affymetrix MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 20261,19455
scde
Single Cell Differential ExpressionEvan Biederstedt		Evan Biederstedtsoftware28 Apr 20261,17950
tricycle
tricycle: Transferable Representation and Inference of cell cycleShijie Zheng		Shijie Zhengsoftware28 Apr 20261,163111
SplicingGraphs
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to themH. Pagès		H. Pagèssoftware28 Apr 20261,16279
mosaics
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)Dongjun Chung		Dongjun Chungsoftware28 Apr 20261,14645
InPAS
Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq dataJianhong Ou		Jianhong Ousoftware28 Apr 20261,145143
SPONGE
Sparse Partial Correlations On Gene ExpressionMarkus List		Markus Listsoftware11 Jun 20261,143187
NanoStringNCTools
NanoString nCounter ToolsMaddy Griswold		Maddy Griswoldsoftware28 Apr 20261,13677