Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "Transcription" keyword
dinoR 1.0.0
Differential NOMe-seq analysis1 version - Latest release: about 1 month ago - 339 downloads total - 0 stars on GitHub - 1 maintainer
mosdef 1.0.0
MOSt frequently used and useful Differential Expression Functions1 version - Latest release: about 1 month ago - 0 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
3 versions - Latest release: about 1 month ago - 8 dependent packages - 34.1 thousand downloads total - 220 stars on GitHub - 1 maintainer
iSEE 2.16.0
Interactive SummarizedExperiment Explorer3 versions - Latest release: about 1 month ago - 8 dependent packages - 34.1 thousand downloads total - 220 stars on GitHub - 1 maintainer
iSEEfier 1.0.0
Streamlining the creation of initial states for starting an iSEE instance1 version - Latest release: about 1 month ago - 295 downloads total - 0 stars on GitHub - 1 maintainer
tidyomics 0.99.7
Easily install and load the tidyomics ecosystem2 versions - Latest release: about 1 month ago - 366 downloads total - 18 stars on GitHub - 1 maintainer
epiregulon 1.0.0
Gene regulatory network inference from single cell epigenomic data1 version - Latest release: about 1 month ago - 1 dependent package - 194 downloads total - 12 stars on GitHub - 1 maintainer
epiregulon.extra 1.0.0
Companion package to epiregulon with additional plotting, differential and graph functions1 version - Latest release: about 1 month ago - 214 downloads total - 0 stars on GitHub - 1 maintainer
RIVER 1.26.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)3 versions - Latest release: 7 months ago - 8.83 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
14 versions - Latest release: 30 days ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R14 versions - Latest release: 30 days ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
Top 0.3% on bioconductor.org
5 versions - Latest release: 30 days ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
limma 3.60.0
Linear Models for Microarray Data5 versions - Latest release: 30 days ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
tidySummarizedExperiment 1.14.0
Brings SummarizedExperiment to the Tidyverse3 versions - Latest release: 20 days ago - 5 dependent packages - 10.5 thousand downloads total - 19 stars on GitHub - 1 maintainer
rTRM 1.40.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks3 versions - Latest release: 7 months ago - 1 dependent package - 20 thousand downloads total - 2 stars on GitHub - 1 maintainer
distinct 1.14.5
distinct: a method for differential analyses via hierarchical permutation tests4 versions - Latest release: 5 months ago - 2 dependent packages - 8.74 thousand downloads total - 11 stars on GitHub - 1 maintainer
TEKRABber 1.6.0
An R package estimates the correlations of orthologs and transposable elements between two species3 versions - Latest release: 7 months ago - 2.73 thousand downloads total - 2 stars on GitHub - 1 maintainer
EventPointer 3.10.0
An effective identification of alternative splicing events using junction arrays and RNA-Seq data3 versions - Latest release: 6 months ago - 11.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
methodical 1.0.0
Discovering genomic regions where methylation is strongly associated with transcriptional activity1 version - Latest release: about 1 month ago - 346 downloads total - 0 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis2 versions - Latest release: 7 months ago - 881 downloads total - 0 stars on GitHub - 1 maintainer
GOexpress 1.36.0
Visualise microarray and RNAseq data using gene ontology annotations3 versions - Latest release: 6 months ago - 1 dependent package - 24.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
primirTSS 1.20.0
Prediction of pri-miRNA Transcription Start Site3 versions - Latest release: 6 months ago - 5.92 thousand downloads total - 0 stars on GitHub - 1 maintainer
ctsGE 1.28.0
Clustering of Time Series Gene Expression data3 versions - Latest release: 6 months ago - 11.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
erccdashboard 1.36.0
Assess Differential Gene Expression Experiments with ERCC Controls3 versions - Latest release: 6 months ago - 19 thousand downloads total - 7 stars on GitHub - 1 maintainer
motifbreakR 2.16.0
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription F...3 versions - Latest release: 6 months ago - 20.3 thousand downloads total - 24 stars on GitHub - 1 maintainer
annmap 1.44.0
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.3 versions - Latest release: 6 months ago - 19.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
planttfhunter 1.2.0
Identification and classification of plant transcription factors3 versions - Latest release: 7 months ago - 1.28 thousand downloads total - 0 stars on GitHub - 1 maintainer
pathwayPCA 1.18.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection3 versions - Latest release: 6 months ago - 1 dependent package - 7.56 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 0.5% on bioconductor.org
4 versions - Latest release: about 1 month ago - 146 dependent packages - 2.78 million downloads total - 330 stars on GitHub - 1 maintainer
DESeq2 1.44.0
Differential gene expression analysis based on the negative binomial distribution4 versions - Latest release: about 1 month ago - 146 dependent packages - 2.78 million downloads total - 330 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
3 versions - Latest release: 27 days ago - 267 thousand downloads total - 384 stars on GitHub - 1 maintainer
EnhancedVolcano 1.22.0
Publication-ready volcano plots with enhanced colouring and labeling3 versions - Latest release: 27 days ago - 267 thousand downloads total - 384 stars on GitHub - 1 maintainer
diffcoexp 1.22.0
Differential Co-expression Analysis3 versions - Latest release: 6 months ago - 10.9 thousand downloads total - 15 stars on GitHub - 1 maintainer
ILoReg 1.12.1
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data4 versions - Latest release: 3 months ago - 3.61 thousand downloads total - 4 stars on GitHub - 1 maintainer
CAGEfightR 1.22.0
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor3 versions - Latest release: 6 months ago - 1 dependent package - 18.7 thousand downloads total - 8 stars on GitHub - 1 maintainer
transcriptogramer 1.24.0
Transcriptional analysis based on transcriptograms3 versions - Latest release: 6 months ago - 8.67 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 8.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 24.6 thousand downloads total - 9 stars on GitHub - 1 maintainer
regionReport 1.36.0
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results3 versions - Latest release: 6 months ago - 1 dependent package - 24.6 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 9.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 2 dependent packages - 29.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
DEFormats 1.30.0
Differential gene expression data formats converter3 versions - Latest release: 6 months ago - 2 dependent packages - 29.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
subSeq 1.32.0
Subsampling of high-throughput sequencing count data3 versions - Latest release: 6 months ago - 14 thousand downloads total - 19 stars on GitHub - 2 maintainers
gg4way 1.0.2
4way Plots of Differential Expression4 versions - Latest release: 3 months ago - 983 downloads total - 0 stars on GitHub - 1 maintainer
GSgalgoR 1.12.0
An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatur...3 versions - Latest release: 6 months ago - 3.83 thousand downloads total - 15 stars on GitHub - 1 maintainer
DifferentialRegulation 2.0.3
Differentially regulated genes from scRNA-seq data6 versions - Latest release: 3 months ago - 2.37 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
3 versions - Latest release: 7 months ago - 13 dependent packages - 360 thousand downloads total - 130 stars on GitHub - 1 maintainer
tximport 1.30.0
Import and summarize transcript-level estimates for transcript- and gene-level analysis3 versions - Latest release: 7 months ago - 13 dependent packages - 360 thousand downloads total - 130 stars on GitHub - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data4 versions - Latest release: 26 days ago - 3.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
motifcounter 1.26.0
R package for analysing TFBSs in DNA sequences3 versions - Latest release: 7 months ago - 20.2 thousand downloads total - 1 maintainer
epidecodeR 1.10.0
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation3 versions - Latest release: 7 months ago - 2.79 thousand downloads total - 3 stars on GitHub - 1 maintainer
quantiseqr 1.10.0
Quantification of the Tumor Immune contexture from RNA-seq data3 versions - Latest release: 7 months ago - 2 dependent packages - 11.8 thousand downloads total - 1 maintainer
MBASED 1.36.0
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expressio...3 versions - Latest release: 7 months ago - 15.9 thousand downloads total - 1 maintainer
IsoformSwitchAnalyzeR 2.2.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...3 versions - Latest release: 7 months ago - 28.3 thousand downloads total - 1 maintainer
tLOH 1.10.0
Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor c...3 versions - Latest release: 7 months ago - 2.68 thousand downloads total - 3 stars on GitHub - 1 maintainer
SPONGE 1.24.0
Sparse Partial Correlations On Gene Expression3 versions - Latest release: 7 months ago - 2 dependent packages - 8.57 thousand downloads total - 1 maintainer
dpeak 1.14.0
dPeak (Deconvolution of Peaks in ChIP-seq Analysis)3 versions - Latest release: 7 months ago - 6.07 thousand downloads total - 0 stars on GitHub - 1 maintainer
TransView 1.46.0
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets3 versions - Latest release: 7 months ago - 21.6 thousand downloads total - 1 maintainer
Guitar 2.18.0
Guitar3 versions - Latest release: 7 months ago - 18.4 thousand downloads total - 1 maintainer
OMICsPCA 1.20.0
An R package for quantitative integration and analysis of multiple omics assays from heterogeneou...3 versions - Latest release: 7 months ago - 7.29 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 39.6 thousand downloads total - 1 maintainer
altcdfenvs 2.64.0
alternative CDF environments (aka probeset mappings)3 versions - Latest release: 7 months ago - 1 dependent package - 39.6 thousand downloads total - 1 maintainer
Linnorm 2.26.0
Linear model and normality based normalization and transformation method (Linnorm)3 versions - Latest release: 7 months ago - 1 dependent package - 22.4 thousand downloads total - 1 maintainer
NanoStringNCTools 1.10.1
NanoString nCounter Tools4 versions - Latest release: about 1 month ago - 2 dependent packages - 14.3 thousand downloads total - 1 maintainer
easier 1.8.0
Estimate Systems Immune Response from RNA-seq data3 versions - Latest release: 7 months ago - 4.36 thousand downloads total - 1 maintainer
CuratedAtlasQueryR 1.2.0
Queries the Human Cell Atlas3 versions - Latest release: 26 days ago - 1.07 thousand downloads total - 77 stars on GitHub - 1 maintainer
ISoLDE 1.30.0
Integrative Statistics of alleLe Dependent Expression3 versions - Latest release: 7 months ago - 9.18 thousand downloads total - 1 maintainer
tigre 1.56.0
Transcription factor Inference through Gaussian process Reconstruction of Expression3 versions - Latest release: 7 months ago - 26.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
BiFET 1.22.0
Bias-free Footprint Enrichment Test3 versions - Latest release: 7 months ago - 8.91 thousand downloads total - 1 maintainer
omicsPrint 1.22.0
Cross omic genetic fingerprinting3 versions - Latest release: 7 months ago - 7.42 thousand downloads total - 1 maintainer
Top 7.4% on bioconductor.org
3 versions - Latest release: 7 months ago - 38 thousand downloads total - 1 maintainer
ELMER 2.26.0
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes3 versions - Latest release: 7 months ago - 38 thousand downloads total - 1 maintainer
crossmeta 1.28.0
Cross Platform Meta-Analysis of Microarray Data3 versions - Latest release: 6 months ago - 1 dependent package - 15.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
ISLET 1.4.0
Individual-Specific ceLl typE referencing Tool3 versions - Latest release: 7 months ago - 1.63 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
3 versions - Latest release: 7 months ago - 3 dependent packages - 28.9 thousand downloads total - 1 maintainer
RTN 2.26.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons3 versions - Latest release: 7 months ago - 3 dependent packages - 28.9 thousand downloads total - 1 maintainer
CeTF 1.14.0
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation an...3 versions - Latest release: 7 months ago - 6.04 thousand downloads total - 1 maintainer
ppcseq 1.10.0
Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models3 versions - Latest release: 7 months ago - 2.85 thousand downloads total - 6 stars on GitHub - 1 maintainer
target 1.16.0
Predict Combined Function of Transcription Factors3 versions - Latest release: 7 months ago - 4.73 thousand downloads total - 4 stars on GitHub - 1 maintainer
SEPIRA 1.22.0 removed
Systems EPigenomics Inference of Regulatory Activity2 versions - Latest release: 7 months ago - 5.66 thousand downloads total - 1 maintainer
NetActivity 1.4.0
Compute gene set scores from a deep learning framework3 versions - Latest release: 7 months ago - 1.6 thousand downloads total - 1 maintainer
CoGAPS 3.22.0
Coordinated Gene Activity in Pattern Sets3 versions - Latest release: 7 months ago - 3 dependent packages - 29.2 thousand downloads total - 4 maintainers
covRNA 1.28.0
Multivariate Analysis of Transcriptomic Data3 versions - Latest release: 7 months ago - 9.83 thousand downloads total - 1 maintainer
ivygapSE 1.24.0
A SummarizedExperiment for Ivy-GAP data3 versions - Latest release: 7 months ago - 7.8 thousand downloads total - 1 maintainer
GSRI 2.50.0
Gene Set Regulation Index3 versions - Latest release: 7 months ago - 25.8 thousand downloads total - 1 maintainer
KBoost 1.10.0
Inference of gene regulatory networks from gene expression data3 versions - Latest release: 7 months ago - 2.94 thousand downloads total - 4 stars on GitHub - 1 maintainer
TFHAZ 1.24.0
Transcription Factor High Accumulation Zones3 versions - Latest release: 7 months ago - 7.41 thousand downloads total - 1 maintainer
snm 1.50.0
Supervised Normalization of Microarrays3 versions - Latest release: 7 months ago - 1 dependent package - 35.5 thousand downloads total - 1 maintainer
SpatialOmicsOverlay 1.2.1
Spatial Overlay for Omic Data from Nanostring GeoMx Data3 versions - Latest release: 7 months ago - 1.68 thousand downloads total - 1 maintainer
cbaf 1.24.0
Automated functions for comparing various omic data from cbioportal.org3 versions - Latest release: 7 months ago - 8.7 thousand downloads total - 1 maintainer
sigFeature 1.20.0
sigFeature: Significant feature selection using SVM-RFE & t-statistic3 versions - Latest release: 7 months ago - 12.7 thousand downloads total - 1 maintainer
ChIPexoQual 1.26.0
ChIPexoQual3 versions - Latest release: 7 months ago - 10.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
aggregateBioVar 1.12.0
Differential Gene Expression Analysis for Multi-subject scRNA-seq3 versions - Latest release: 7 months ago - 5.15 thousand downloads total - 5 stars on GitHub - 1 maintainer
enrichTF 1.18.0
Transcription Factors Enrichment Analysis3 versions - Latest release: 7 months ago - 6.82 thousand downloads total - 2 stars on GitHub - 1 maintainer
proActiv 1.12.0
Estimate Promoter Activity from RNA-Seq data3 versions - Latest release: 7 months ago - 4.46 thousand downloads total - 44 stars on GitHub - 1 maintainer
ExiMiR 2.44.0
R functions for the normalization of Exiqon miRNA array data3 versions - Latest release: 7 months ago - 24.8 thousand downloads total - 1 maintainer
QuaternaryProd 1.36.0
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs3 versions - Latest release: 7 months ago - 12.3 thousand downloads total - 1 maintainer
Harman 1.30.0
The removal of batch effects from datasets using a PCA and constrained optimisation based technique3 versions - Latest release: 7 months ago - 1 dependent package - 20.4 thousand downloads total - 1 maintainer
ERSSA 1.20.0
Empirical RNA-seq Sample Size Analysis3 versions - Latest release: 7 months ago - 6.38 thousand downloads total - 0 stars on GitHub - 1 maintainer
ASpli 2.12.0
Analysis of Alternative Splicing Using RNA-Seq3 versions - Latest release: 7 months ago - 1 dependent package - 17 thousand downloads total - 1 maintainer
customProDB 1.42.1
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics ...4 versions - Latest release: 2 months ago - 26 thousand downloads total - 1 maintainer
GSALightning 1.30.0
Fast Permutation-based Gene Set Analysis3 versions - Latest release: 7 months ago - 10.1 thousand downloads total - 5 stars on GitHub - 1 maintainer
AMARETTO 1.18.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...3 versions - Latest release: 7 months ago - 7.55 thousand downloads total - 1 maintainer
bambu 3.4.1
Context-Aware Transcript Quantification from Long Read RNA-Seq data4 versions - Latest release: about 1 month ago - 1 dependent package - 13 thousand downloads total - 118 stars on GitHub - 1 maintainer
RgnTX 1.4.0
Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and am...3 versions - Latest release: 7 months ago - 1.6 thousand downloads total - 1 maintainer
GRaNIE 1.6.1
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...3 versions - Latest release: 7 months ago - 3.75 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
3 versions - Latest release: 7 months ago - 3 dependent packages - 42.5 thousand downloads total - 1 maintainer
SGSeq 1.36.0
Splice event prediction and quantification from RNA-seq data3 versions - Latest release: 7 months ago - 3 dependent packages - 42.5 thousand downloads total - 1 maintainer
wiggleplotr 1.26.0
Make read coverage plots from BigWig files3 versions - Latest release: 7 months ago - 1 dependent package - 14.7 thousand downloads total - 1 maintainer
IMAS 1.26.0
Integrative analysis of Multi-omics data for Alternative Splicing3 versions - Latest release: 7 months ago - 9.74 thousand downloads total - 1 maintainer
BRGenomics 1.14.1
Tools for the Efficient Analysis of High-Resolution Genomics Data4 versions - Latest release: 2 months ago - 1 dependent package - 8.07 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 41.4 thousand downloads total - 1 maintainer
BicARE 1.60.0
Biclustering Analysis and Results Exploration3 versions - Latest release: 7 months ago - 1 dependent package - 41.4 thousand downloads total - 1 maintainer
RegEnrich 1.12.1
Gene regulator enrichment analysis4 versions - Latest release: about 1 month ago - 4.65 thousand downloads total - 1 maintainer
ATACCoGAPS 1.4.0
Analysis Tools for scATACseq Data with CoGAPS3 versions - Latest release: 7 months ago - 1.55 thousand downloads total - 4 stars on GitHub - 1 maintainer
Related Keywords
Software
188
GeneExpression
133
RNASeq
96
Sequencing
84
DifferentialExpression
75
ImmunoOncology
62
Transcriptomics
61
GeneRegulation
42
Visualization
42
Microarray
38
Clustering
37
GeneSetEnrichment
32
Genetics
31
MultipleComparison
29
Regression
28
SingleCell
28
Normalization
28
FunctionalGenomics
27
AlternativeSplicing
26
Coverage
26
DataImport
25
ChIPSeq
23
Preprocessing
22
QualityControl
21
Network
20
SystemsBiology
19
DifferentialSplicing
19
Epigenetics
19
Bayesian
18
BiomedicalInformatics
17
NetworkInference
16
GraphAndNetwork
16
TimeCourse
15
BatchEffect
15
bioconductor
14
Pathways
13
Annotation
13
DimensionReduction
13
StatisticalMethod
13
Classification
12
PrincipalComponent
12
r
12
mRNAMicroarray
12
FeatureExtraction
11
GUI
11
OneChannel
11
DataRepresentation
11
GeneTarget
11
Proteomics
10
DNAMethylation
10
CellBiology
10
ProprietaryPlatforms
9
transcriptomics
9
SNP
9
GeneticVariability
8
ReportWriting
8
MotifAnnotation
7
TwoChannel
7
ATACSeq
7
BiologicalQuestion
7
Alignment
7
FunctionalPrediction
7
CellBasedAssays
7
GO
7
DifferentialMethylation
6
PeakDetection
6
AssayDomain
5
Infrastructure
5
ExonArray
5
WorkflowStep
5
GenomeAnnotation
5
rstats
5
Survival
5
CopyNumberVariation
5
gene-expression
4
MicroRNAArray
4
Metabolomics
4
ShinyApps
4
MethylSeq
4
human-cell-atlas
4
FlowCytometry
4
rnaseq
4
genomics
4
deseq2
4
ChipOnChip
4
bioconductor-package
4
GenePrediction
4
MethylationArray
3
edger
3
MassSpectrometry
3
single-cell-rna-seq
3
transcription-factors
3
HiddenMarkovModel
3
KEGG
3
SequenceMatching
3
rna-seq-data
3
differential-expression
3
SupportVectorMachine
3
NetworkEnrichment
3
SplicedAlignment
3