Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "FunctionalGenomics" keyword
MIRA 1.24.0
Methylation-Based Inference of Regulatory Activity3 versions - Latest release: 6 months ago - 1 dependent package - 10.5 thousand downloads total - 1 maintainer
Top 1.5% on bioconductor.org
3 versions - Latest release: 20 days ago - 9 dependent packages - 226 thousand downloads total - 421 stars on GitHub - 1 maintainer
maftools 2.20.0 💰
Summarize, Analyze and Visualize MAF Files3 versions - Latest release: 20 days ago - 9 dependent packages - 226 thousand downloads total - 421 stars on GitHub - 1 maintainer
AlphaMissenseR 1.0.0
Accessing AlphaMissense Data Resources in R2 versions - Latest release: 21 days ago - 358 downloads total - 5 stars on GitHub - 1 maintainer
epidecodeR 1.10.0
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation3 versions - Latest release: 6 months ago - 2.79 thousand downloads total - 3 stars on GitHub - 1 maintainer
IsoformSwitchAnalyzeR 2.2.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...3 versions - Latest release: 6 months ago - 28.3 thousand downloads total - 1 maintainer
syntenet 1.4.2
Inference And Analysis Of Synteny Networks4 versions - Latest release: about 1 month ago - 1 dependent package - 3.4 thousand downloads total - 14 stars on GitHub - 1 maintainer
OMICsPCA 1.20.0
An R package for quantitative integration and analysis of multiple omics assays from heterogeneou...3 versions - Latest release: 6 months ago - 7.29 thousand downloads total - 1 maintainer
chipenrich 2.26.0
Gene Set Enrichment For ChIP-seq Peak Data3 versions - Latest release: 6 months ago - 27.8 thousand downloads total - 1 maintainer
QTLExperiment 1.0.0
S4 classes for QTL summary statistics and metadata2 versions - Latest release: 7 months ago - 1 dependent package - 840 downloads total - 1 stars on GitHub - 1 maintainer
nullranges 1.8.0
Generation of null ranges via bootstrapping or covariate matching3 versions - Latest release: 6 months ago - 1 dependent package - 4.44 thousand downloads total - 22 stars on GitHub - 1 maintainer
BasicSTARRseq 1.30.0
Basic peak calling on STARR-seq data3 versions - Latest release: 6 months ago - 12 thousand downloads total - 1 maintainer
RITAN 1.26.0
Rapid Integration of Term Annotation and Network resources3 versions - Latest release: 6 months ago - 9.59 thousand downloads total - 1 maintainer
GenomicDistributions 1.10.0
GenomicDistributions: fast analysis of genomic intervals with Bioconductor3 versions - Latest release: 6 months ago - 4.62 thousand downloads total - 1 maintainer
idr2d 1.16.0
Irreproducible Discovery Rate for Genomic Interactions Data3 versions - Latest release: 6 months ago - 5.25 thousand downloads total - 1 maintainer
miloR 2.0.0
Differential neighbourhood abundance testing on a graph3 versions - Latest release: 20 days ago - 10.9 thousand downloads total - 310 stars on GitHub - 1 maintainer
dmrseq 1.22.1
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing4 versions - Latest release: 2 months ago - 1 dependent package - 17.9 thousand downloads total - 1 maintainer
NetActivity 1.4.0
Compute gene set scores from a deep learning framework3 versions - Latest release: 6 months ago - 1.6 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 32.7 thousand downloads total - 1 maintainer
MAGeCKFlute 2.6.0
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens3 versions - Latest release: 6 months ago - 1 dependent package - 32.7 thousand downloads total - 1 maintainer
rDGIdb 1.28.0
R Wrapper for DGIdb3 versions - Latest release: 6 months ago - 11.6 thousand downloads total - 1 maintainer
mpra 1.24.0
Analyze massively parallel reporter assays3 versions - Latest release: 6 months ago - 8.48 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 51.2 thousand downloads total - 1 maintainer
hpar 1.44.0
Human Protein Atlas in R3 versions - Latest release: 6 months ago - 3 dependent packages - 51.2 thousand downloads total - 1 maintainer
proActiv 1.12.0
Estimate Promoter Activity from RNA-Seq data3 versions - Latest release: 6 months ago - 4.46 thousand downloads total - 44 stars on GitHub - 1 maintainer
crisprScore 1.6.0
On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs3 versions - Latest release: 6 months ago - 3 dependent packages - 5 thousand downloads total - 9 stars on GitHub - 1 maintainer
LOLA 1.32.0
Locus overlap analysis for enrichment of genomic ranges3 versions - Latest release: 6 months ago - 5 dependent packages - 25 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 26.8 thousand downloads total - 1 maintainer
FGNet 3.36.0
Functional Gene Networks derived from biological enrichment analyses3 versions - Latest release: 6 months ago - 1 dependent package - 26.8 thousand downloads total - 1 maintainer
AlphaBeta 1.16.0
Computational inference of epimutation rates and spectra from high-throughput DNA methylation dat...3 versions - Latest release: 6 months ago - 7.43 thousand downloads total - 1 maintainer
CexoR 1.40.0
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates3 versions - Latest release: 6 months ago - 18.6 thousand downloads total - 1 maintainer
EGAD 1.30.0
Extending guilt by association by degree3 versions - Latest release: 6 months ago - 13.4 thousand downloads total - 1 maintainer
VarCon 1.10.0
VarCon: an R package for retrieving neighboring nucleotides of an SNV3 versions - Latest release: 6 months ago - 2.8 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
Cogito 1.8.0
Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic...3 versions - Latest release: 6 months ago - 2.39 thousand downloads total - 1 maintainer
normr 1.28.0
Normalization and difference calling in ChIP-seq data3 versions - Latest release: 6 months ago - 15.7 thousand downloads total - 11 stars on GitHub - 1 maintainer
chromPlot 1.30.0
Global visualization tool of genomic data3 versions - Latest release: 6 months ago - 16 thousand downloads total - 1 maintainer
spatzie 1.8.0
Identification of enriched motif pairs from chromatin interaction data3 versions - Latest release: 6 months ago - 2.36 thousand downloads total - 1 maintainer
heatmaps 1.26.0
Flexible Heatmaps for Functional Genomics and Sequence Features3 versions - Latest release: 6 months ago - 1 dependent package - 26.6 thousand downloads total - 1 maintainer
BindingSiteFinder 2.0.0
Binding site defintion based on iCLIP data3 versions - Latest release: 6 months ago - 2.89 thousand downloads total - 3 stars on GitHub - 1 maintainer
sincell 1.34.0
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data3 versions - Latest release: 6 months ago - 15.2 thousand downloads total - 1 maintainer
crisprBowtie 1.6.0
Bowtie-based alignment of CRISPR gRNA spacer sequences3 versions - Latest release: 6 months ago - 2 dependent packages - 4.72 thousand downloads total - 1 stars on GitHub - 1 maintainer
mariner 1.2.0
Mariner: Explore the Hi-Cs3 versions - Latest release: 6 months ago - 1.39 thousand downloads total - 1 maintainer
rfaRm 1.14.2
An R interface to the Rfam database5 versions - Latest release: 3 months ago - 4.46 thousand downloads total - 2 maintainers
pfamAnalyzeR 1.2.0
Identification of domain isotypes in pfam data3 versions - Latest release: 6 months ago - 1 dependent package - 4.36 thousand downloads total - 1 stars on GitHub - 1 maintainer
gCrisprTools 2.8.0
Suite of Functions for Pooled Crispr Screen QC and Analysis3 versions - Latest release: 6 months ago - 11.6 thousand downloads total - 1 maintainer
crisprBwa 1.6.0
BWA-based alignment of CRISPR gRNA spacer sequences3 versions - Latest release: 6 months ago - 1 dependent package - 2.59 thousand downloads total - 1 stars on GitHub - 1 maintainer
metaseqR2 1.14.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...3 versions - Latest release: 6 months ago - 5.12 thousand downloads total - 1 maintainer
GenomicOZone 1.16.0
Delineate outstanding genomic zones of differential gene activity3 versions - Latest release: 6 months ago - 5.21 thousand downloads total - 1 maintainer
Top 10.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 2 dependent packages - 31.5 thousand downloads total - 1 maintainer
CAGEr 2.8.0
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcr...3 versions - Latest release: 6 months ago - 2 dependent packages - 31.5 thousand downloads total - 1 maintainer
fCCAC 1.28.0
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing ...3 versions - Latest release: 6 months ago - 9.84 thousand downloads total - 1 maintainer
atena 1.8.0
Analysis of Transposable Elements3 versions - Latest release: 6 months ago - 4.17 thousand downloads total - 5 stars on GitHub - 1 maintainer
COCOA 2.16.0
Coordinate Covariation Analysis3 versions - Latest release: 6 months ago - 7.09 thousand downloads total - 1 maintainer
airpart 1.10.0
Differential cell-type-specific allelic imbalance3 versions - Latest release: 6 months ago - 3.63 thousand downloads total - 2 stars on GitHub - 1 maintainer
dreamlet 1.2.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...3 versions - Latest release: 16 days ago - 1.21 thousand downloads total - 9 stars on GitHub - 1 maintainer
variancePartition 1.34.0
Quantify and interpret drivers of variation in multilevel gene expression experiments5 versions - Latest release: 15 days ago - 4 dependent packages - 57.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
coMET 1.34.0
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methyl...3 versions - Latest release: 6 months ago - 21.1 thousand downloads total - 1 maintainer
ORFik 1.22.2
Open Reading Frames in Genomics5 versions - Latest release: 3 months ago - 2 dependent packages - 16.3 thousand downloads total - 32 stars on GitHub - 1 maintainer
crisprDesign 1.4.0
Comprehensive design of CRISPR gRNAs for nucleases and base editors3 versions - Latest release: 6 months ago - 3 dependent packages - 4 thousand downloads total - 15 stars on GitHub - 1 maintainer
OmaDB 2.20.0
R wrapper for the OMA REST API3 versions - Latest release: 5 days ago - 2 dependent packages - 11.4 thousand downloads total - 1 stars on GitHub - 2 maintainers
screenCounter 1.4.0
Counting Reads in High-Throughput Sequencing Screens3 versions - Latest release: 5 days ago - 1.22 thousand downloads total - 3 stars on GitHub - 1 maintainer
sitadela 1.12.0
An R package for the easy provision of simple but complete tab-delimited genomic annotation from ...3 versions - Latest release: 8 days ago - 2.78 thousand downloads total - 0 stars on GitHub - 1 maintainer
plotgardener 1.10.0
Coordinate-Based Genomic Visualization Package for R6 versions - Latest release: 16 days ago - 4 dependent packages - 9.68 thousand downloads total - 276 stars on GitHub - 1 maintainer
decoupleR 2.9.7
decoupleR: Ensemble of computational methods to infer biological activities from omics data3 versions - Latest release: 7 days ago - 3 dependent packages - 25.4 thousand downloads total - 154 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
7 versions - Latest release: 7 days ago - 3 dependent packages - 93 thousand downloads total - 64 stars on GitHub - 1 maintainer
tximeta 1.22.1
Transcript Quantification Import with Automatic Metadata7 versions - Latest release: 7 days ago - 3 dependent packages - 93 thousand downloads total - 64 stars on GitHub - 1 maintainer
crisprViz 1.6.0
Visualization Functions for CRISPR gRNAs3 versions - Latest release: 7 days ago - 2 dependent packages - 3.21 thousand downloads total - 4 stars on GitHub - 1 maintainer
eisaR 1.16.0
Exon-Intron Split Analysis (EISA) in R4 versions - Latest release: 7 days ago - 7.62 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
4 versions - Latest release: 19 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
limma 3.60.0
Linear Models for Microarray Data4 versions - Latest release: 19 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
14 versions - Latest release: 19 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R14 versions - Latest release: 19 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
crisprBase 1.6.0
Base functions and classes for CRISPR gRNA design2 versions - Latest release: 7 months ago - 6 dependent packages - 4.34 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
2 versions - Latest release: 6 months ago - 6 dependent packages - 57.5 thousand downloads total - 25 stars on GitHub - 1 maintainer
annotatr 1.28.0
Annotation of Genomic Regions to Genomic Annotations2 versions - Latest release: 6 months ago - 6 dependent packages - 57.5 thousand downloads total - 25 stars on GitHub - 1 maintainer
InterMineR 1.26.0
R Interface with InterMine-Powered Databases4 versions - Latest release: 12 days ago - 10.4 thousand downloads total - 17 stars on GitHub - 1 maintainer
gDNAx 1.2.0
Diagnostics for assessing genomic DNA contamination in RNA-seq data4 versions - Latest release: 12 days ago - 1.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
3 versions - Latest release: 13 days ago - 2 dependent packages - 227 thousand downloads total - 1 maintainer
DiffBind 3.14.0
Differential Binding Analysis of ChIP-Seq Peak Data3 versions - Latest release: 13 days ago - 2 dependent packages - 227 thousand downloads total - 1 maintainer
memes 1.12.0
motif matching, comparison, and de novo discovery using the MEME Suite3 versions - Latest release: 13 days ago - 8.72 thousand downloads total - 43 stars on GitHub - 1 maintainer
cogeqc 1.8.0
Systematic quality checks on comparative genomics analyses4 versions - Latest release: 14 days ago - 2.43 thousand downloads total - 8 stars on GitHub - 1 maintainer
cageminer 1.10.0
Candidate Gene Miner3 versions - Latest release: 14 days ago - 2.64 thousand downloads total - 1 stars on GitHub - 1 maintainer
doubletrouble 1.4.0
Identification and classification of duplicated genes6 versions - Latest release: 14 days ago - 1.65 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
7 versions - Latest release: 14 days ago - 15 dependent packages - 382 thousand downloads total - 164 stars on GitHub - 1 maintainer
GSVA 1.52.1
Gene Set Variation Analysis for Microarray and RNA-Seq Data7 versions - Latest release: 14 days ago - 15 dependent packages - 382 thousand downloads total - 164 stars on GitHub - 1 maintainer
crisprVerse 1.6.0
Easily install and load the crisprVerse ecosystem for CRISPR gRNA design3 versions - Latest release: 20 days ago - 2.4 thousand downloads total - 7 stars on GitHub - 1 maintainer
zenith 1.6.0
Gene set analysis following differential expression using linear (mixed) modeling with dream4 versions - Latest release: 14 days ago - 2 dependent packages - 3.42 thousand downloads total - 0 stars on GitHub - 1 maintainer
GenomAutomorphism 1.6.0
Compute the automorphisms between DNA's Abelian group representations3 versions - Latest release: 17 days ago - 1.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
proteasy 1.6.0
Protease Mapping3 versions - Latest release: 17 days ago - 1.07 thousand downloads total - 2 stars on GitHub - 1 maintainer
EWCE 1.12.0
Expression Weighted Celltype Enrichment4 versions - Latest release: 20 days ago - 8.86 thousand downloads total - 51 stars on GitHub - 1 maintainer
MIRit 0.99.13
Integrate microRNA and gene expression to decipher pathway complexity1 version - Latest release: 21 days ago - 151 downloads total - 0 stars on GitHub - 1 maintainer
multistateQTL 1.0.0
Toolkit for the analysis of multi-state QTL data1 version - Latest release: 21 days ago - 0 stars on GitHub - 1 maintainer
crisprShiny 1.0.0
Exploring curated CRISPR gRNAs via Shiny1 version - Latest release: 21 days ago - 164 downloads total - 1 stars on GitHub - 1 maintainer
HybridExpress 1.0.0
Comparative analysis of RNA-seq data for hybrids and their progenitors1 version - Latest release: 21 days ago - 143 downloads total - 0 stars on GitHub - 1 maintainer
SurfR 0.99.54
Surface Protein Prediction and Identification1 version - Latest release: 21 days ago - 129 downloads total - 0 stars on GitHub - 1 maintainer
RIVER 1.26.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)2 versions - Latest release: 6 months ago - 8.53 thousand downloads total - 10 stars on GitHub - 1 maintainer
ModCon 1.10.0
Modifying splice site usage by changing the mRNP code, while maintaining the genetic code2 versions - Latest release: 6 months ago - 2.39 thousand downloads total - 1 stars on GitHub - 1 maintainer
DEWSeq 1.16.2
Differential Expressed Windows Based on Negative Binomial Distribution2 versions - Latest release: 6 months ago - 5.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis1 version - Latest release: 7 months ago - 569 downloads total - 0 stars on GitHub - 1 maintainer
preciseTAD 1.12.0
preciseTAD: A machine learning framework for precise TAD boundary prediction2 versions - Latest release: 6 months ago - 3.45 thousand downloads total - 6 stars on GitHub - 1 maintainer
planttfhunter 1.2.0
Identification and classification of plant transcription factors2 versions - Latest release: 7 months ago - 949 downloads total - 0 stars on GitHub - 1 maintainer
sevenC 1.22.0
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs2 versions - Latest release: 6 months ago - 7.1 thousand downloads total - 11 stars on GitHub - 1 maintainer
pathwayPCA 1.18.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection2 versions - Latest release: 6 months ago - 1 dependent package - 7.17 thousand downloads total - 11 stars on GitHub - 1 maintainer
loci2path 1.22.0
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs2 versions - Latest release: 6 months ago - 6.84 thousand downloads total - 1 stars on GitHub - 1 maintainer
MOMA 1.14.0
Multi Omic Master Regulator Analysis2 versions - Latest release: 6 months ago - 4.35 thousand downloads total - 5 stars on GitHub - 1 maintainer
MouseFM 1.12.0
In-silico methods for genetic finemapping in inbred mice2 versions - Latest release: 6 months ago - 4.98 thousand downloads total - 0 stars on GitHub - 1 maintainer
DepInfeR 1.6.0
Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and...2 versions - Latest release: 6 months ago - 1.54 thousand downloads total - 0 stars on GitHub - 1 maintainer
ncRNAtools 1.12.0
An R toolkit for non-coding RNA2 versions - Latest release: 6 months ago - 3.27 thousand downloads total - 1 stars on GitHub - 1 maintainer
EpiCompare 1.6.7
Comparison, Benchmarking & QC of Epigenomic Datasets8 versions - Latest release: about 1 month ago - 2.02 thousand downloads total - 12 stars on GitHub - 1 maintainer
GeneAccord 1.18.0 removed
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients1 version - Latest release: 7 months ago - 4.41 thousand downloads total - 2 stars on GitHub - 1 maintainer
Related Keywords
Software
101
Sequencing
35
GeneExpression
32
RNASeq
28
Transcription
27
Epigenetics
25
SystemsBiology
24
Visualization
23
GeneRegulation
23
GeneSetEnrichment
21
DifferentialExpression
21
Transcriptomics
21
ImmunoOncology
20
BiomedicalInformatics
17
Regression
17
DataImport
17
MultipleComparison
16
ChIPSeq
16
Genetics
16
Clustering
14
FunctionalPrediction
14
Coverage
13
QualityControl
13
Preprocessing
13
AlternativeSplicing
12
Normalization
12
Annotation
12
Pathways
11
CellBiology
11
CRISPR
11
GenomeAnnotation
10
Network
10
Classification
10
BatchEffect
9
Microarray
9
SNP
9
bioconductor
9
bioconductor-package
8
GeneTarget
8
Proteomics
8
grna-sequence
7
grna
7
SingleCell
7
grna-sequences
7
crispr-design
7
crispr
7
ATACSeq
7
genomics
7
GenePrediction
7
DNAMethylation
6
Alignment
6
Bayesian
6
crispr-target
6
GenomicVariation
6
PeakDetection
6
NetworkEnrichment
6
ComparativeGenomics
6
HiC
6
DifferentialSplicing
6
r
5
GenomeWideAssociation
5
FeatureExtraction
5
crispr-cas9
5
GO
5
DataRepresentation
5
HistoneModification
5
DifferentialMethylation
5
MethylSeq
5
sgrna
5
sgrna-design
5
GraphAndNetwork
5
rstats
5
TranscriptomeVariant
4
NetworkInference
4
bioinformatics
4
VariantAnnotation
4
WholeGenome
4
TimeCourse
4
DNaseSeq
4
crispr-analysis
4
PrincipalComponent
4
MathematicalBiology
4
Survival
3
ReportWriting
3
ProprietaryPlatforms
3
WorkflowStep
3
Pharmacogenomics
3
Pharmacogenetics
3
DifferentialPeakCalling
3
r-package
3
Metabolomics
3
OneChannel
3
mRNAMicroarray
3
GeneticVariability
3
comparative-genomics
3
Phylogenetics
3
DNA3DStructure
3
GenomeAssembly
3
PatternLogic
2
GUI
2