Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "bioinformatics" keyword
sparrow 1.10.0
Take command of set enrichment analyses through a unified interface4 versions - Latest release: about 1 month ago - 1 dependent package - 4.36 thousand downloads total - 20 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
4 versions - Latest release: about 1 month ago - 30 dependent packages - 397 thousand downloads total - 120 stars on GitHub - 1 maintainer
MSnbase 2.30.1
Base Functions and Classes for Mass Spectrometry and Proteomics4 versions - Latest release: about 1 month ago - 30 dependent packages - 397 thousand downloads total - 120 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
3 versions - Latest release: 30 days ago - 47 dependent packages - 1.87 million downloads total - 82 stars on GitHub - 1 maintainer
GEOquery 2.72.0
Get data from NCBI Gene Expression Omnibus (GEO)3 versions - Latest release: 30 days ago - 47 dependent packages - 1.87 million downloads total - 82 stars on GitHub - 1 maintainer
DEWSeq 1.16.2
Differential Expressed Windows Based on Negative Binomial Distribution3 versions - Latest release: 7 months ago - 5.52 thousand downloads total - 3 stars on GitHub - 1 maintainer
RLSeq 1.6.0
RLSeq: An analysis package for R-loop mapping data3 versions - Latest release: 8 months ago - 2.39 thousand downloads total - 2 stars on GitHub - 1 maintainer
cogena 1.36.0
co-expressed gene-set enrichment analysis3 versions - Latest release: 7 months ago - 17.9 thousand downloads total - 12 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
getDEE2 1.12.0
Programmatic access to the DEE2 RNA expression dataset3 versions - Latest release: 7 months ago - 4.01 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
3 versions - Latest release: about 1 month ago - 9 dependent packages - 227 thousand downloads total - 423 stars on GitHub - 1 maintainer
maftools 2.20.0 💰
Summarize, Analyze and Visualize MAF Files3 versions - Latest release: about 1 month ago - 9 dependent packages - 227 thousand downloads total - 423 stars on GitHub - 1 maintainer
pathlinkR 1.0.0
Analyze and interpret RNA-Seq results1 version - Latest release: about 1 month ago - 446 downloads total - 4 stars on GitHub - 1 maintainer
geneXtendeR 1.28.0
Optimized Functional Annotation Of ChIP-seq Data3 versions - Latest release: 6 months ago - 13.5 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
3 versions - Latest release: 25 days ago - 2 dependent packages - 730 thousand downloads total - 455 stars on GitHub - 1 maintainer
dada2 1.32.0
Accurate, high-resolution sample inference from amplicon sequencing data3 versions - Latest release: 25 days ago - 2 dependent packages - 730 thousand downloads total - 455 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 11 dependent packages - 233 thousand downloads total - 5 stars on GitHub - 1 maintainer
graphite 1.48.0
GRAPH Interaction from pathway Topological Environment3 versions - Latest release: 6 months ago - 11 dependent packages - 233 thousand downloads total - 5 stars on GitHub - 1 maintainer
biobtreeR 1.14.0
Using biobtree tool from R3 versions - Latest release: 6 months ago - 5.32 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 65.1 thousand downloads total - 38 stars on GitHub - 1 maintainer
singscore 1.22.0
Rank-based single-sample gene set scoring method3 versions - Latest release: 6 months ago - 3 dependent packages - 65.1 thousand downloads total - 38 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.22.0
Random walk with restart on multiplex and heterogeneous Networks3 versions - Latest release: 6 months ago - 1 dependent package - 9.5 thousand downloads total - 17 stars on GitHub - 1 maintainer
ontoProc 1.24.0
processing of ontologies of anatomy, cell lines, and so on3 versions - Latest release: 7 months ago - 3 dependent packages - 13.6 thousand downloads total - 2 stars on GitHub - 1 maintainer
SGCP 1.2.0
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...3 versions - Latest release: 7 months ago - 1.85 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
3 versions - Latest release: 7 months ago - 6 dependent packages - 42.6 thousand downloads total - 205 stars on GitHub - 1 maintainer
splatter 1.26.0
Simple Simulation of Single-cell RNA Sequencing Data3 versions - Latest release: 7 months ago - 6 dependent packages - 42.6 thousand downloads total - 205 stars on GitHub - 1 maintainer
scruff 1.20.0
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)3 versions - Latest release: 6 months ago - 7.81 thousand downloads total - 8 stars on GitHub - 1 maintainer
decontam 1.22.0
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data3 versions - Latest release: 6 months ago - 1 dependent package - 59.3 thousand downloads total - 133 stars on GitHub - 1 maintainer
CiteFuse 1.14.0
CiteFuse: multi-modal analysis of CITE-seq data3 versions - Latest release: 6 months ago - 1 dependent package - 6.89 thousand downloads total - 25 stars on GitHub - 1 maintainer
CellBench 1.18.0
Construct Benchmarks for Single Cell Analysis Methods3 versions - Latest release: 6 months ago - 2 dependent packages - 9.18 thousand downloads total - 28 stars on GitHub - 1 maintainer
orthogene 1.8.0
Interspecies gene mapping3 versions - Latest release: 7 months ago - 1 dependent package - 10.4 thousand downloads total - 35 stars on GitHub - 1 maintainer
BioCor 1.26.0
Functional similarities3 versions - Latest release: 7 months ago - 11.8 thousand downloads total - 14 stars on GitHub - 1 maintainer
gemma.R 3.0.3
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...6 versions - Latest release: 17 days ago - 2.01 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 5.6% on bioconductor.org
3 versions - Latest release: 21 days ago - 4 dependent packages - 50.3 thousand downloads total - 48 stars on GitHub - 1 maintainer
sesame 1.22.0
SEnsible Step-wise Analysis of DNA MEthylation BeadChips3 versions - Latest release: 21 days ago - 4 dependent packages - 50.3 thousand downloads total - 48 stars on GitHub - 1 maintainer
rBLAST 1.0.0
R Interface for the Basic Local Alignment Search Tool1 version - Latest release: about 1 month ago - 182 downloads total - 100 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
3 versions - Latest release: 29 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 stars on GitHub - 1 maintainer
karyoploteR 1.30.0
Plot customizable linear genomes displaying arbitrary data3 versions - Latest release: 29 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 stars on GitHub - 1 maintainer
GEOfastq 1.10.0
Downloads ENA Fastqs With GEO Accessions3 versions - Latest release: 7 months ago - 3.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
methylInheritance 1.26.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...3 versions - Latest release: 7 months ago - 1 dependent package - 9.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
methrix 1.16.0
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing3 versions - Latest release: 7 months ago - 1 dependent package - 6.26 thousand downloads total - 27 stars on GitHub - 1 maintainer
mimager 1.26.0
mimager: The Microarray Imager3 versions - Latest release: 7 months ago - 9.09 thousand downloads total - 0 stars on GitHub - 1 maintainer
packFinder 1.14.0
de novo Annotation of Pack-TYPE Transposable Elements3 versions - Latest release: 7 months ago - 4.39 thousand downloads total - 5 stars on GitHub - 1 maintainer
sevenbridges 1.32.0
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R3 versions - Latest release: 7 months ago - 14.3 thousand downloads total - 33 stars on GitHub - 1 maintainer
CopyNumberPlots 1.18.0
Create Copy-Number Plots using karyoploteR functionality3 versions - Latest release: 7 months ago - 2 dependent packages - 9.48 thousand downloads total - 6 stars on GitHub - 1 maintainer
rmelting 1.18.0
R Interface to MELTING 53 versions - Latest release: 7 months ago - 6.43 thousand downloads total - 2 stars on GitHub - 1 maintainer
TDbasedUFE 1.2.0
Tensor Decomposition Based Unsupervised Feature Extraction3 versions - Latest release: 7 months ago - 1 dependent package - 1.75 thousand downloads total - 5 stars on GitHub - 1 maintainer
TDbasedUFEadv 1.2.0
Advanced package of tensor decomposition based unsupervised feature extraction3 versions - Latest release: 7 months ago - 1.55 thousand downloads total - 0 stars on GitHub - 1 maintainer
deco 1.18.0 removed
Decomposing Heterogeneous Cohorts using Omic Data Profiling2 versions - Latest release: 7 months ago - 4.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
cmapR 1.14.0
CMap Tools in R3 versions - Latest release: 7 months ago - 21.4 thousand downloads total - 78 stars on GitHub - 1 maintainer
epistack 1.8.0
Heatmaps of Stack Profiles from Epigenetic Signals3 versions - Latest release: 7 months ago - 2.46 thousand downloads total - 6 stars on GitHub - 1 maintainer
cfDNAPro 1.8.0
cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-fr...3 versions - Latest release: 7 months ago - 3.41 thousand downloads total - 22 stars on GitHub - 1 maintainer
NormalyzerDE 1.20.0
Evaluation of normalization methods and calculation of differential expression analysis statistics3 versions - Latest release: 6 months ago - 12.2 thousand downloads total - 18 stars on GitHub - 1 maintainer
ClustIRR 1.2.0
Clustering of immune receptor repertoires2 versions - Latest release: 16 days ago - 901 downloads total - 2 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
7 versions - Latest release: 17 days ago - 11 dependent packages - 86.6 thousand downloads total - 42 stars on GitHub - 1 maintainer
SeqArray 1.44.0
Data Management of Large-Scale Whole-Genome Sequence Variant Calls7 versions - Latest release: 17 days ago - 11 dependent packages - 86.6 thousand downloads total - 42 stars on GitHub - 1 maintainer
netSmooth 1.24.0
Network smoothing for scRNAseq3 versions - Latest release: 18 days ago - 1 dependent package - 8.4 thousand downloads total - 26 stars on GitHub - 1 maintainer
signeR 2.6.0
Empirical Bayesian approach to mutational signature discovery3 versions - Latest release: 18 days ago - 14.2 thousand downloads total - 13 stars on GitHub - 1 maintainer
rWikiPathways 1.24.0
rWikiPathways - R client library for the WikiPathways API3 versions - Latest release: 19 days ago - 5 dependent packages - 56.6 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 4.1% on bioconductor.org
3 versions - Latest release: about 1 month ago - 3 dependent packages - 92.3 thousand downloads total - 82 stars on GitHub - 1 maintainer
GenomicDataCommons 1.28.0
NIH / NCI Genomic Data Commons Access3 versions - Latest release: about 1 month ago - 3 dependent packages - 92.3 thousand downloads total - 82 stars on GitHub - 1 maintainer
scMerge 1.20.0
scMerge: Merging multiple batches of scRNA-seq data3 versions - Latest release: 21 days ago - 2 dependent packages - 23.4 thousand downloads total - 62 stars on GitHub - 1 maintainer
POMA 1.14.0
Tools for Omics Data Analysis3 versions - Latest release: 22 days ago - 1 dependent package - 4.86 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 3.2% on bioconductor.org
4 versions - Latest release: 22 days ago - 11 dependent packages - 175 thousand downloads total - 96 stars on GitHub - 1 maintainer
SNPRelate 1.38.0
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data4 versions - Latest release: 22 days ago - 11 dependent packages - 175 thousand downloads total - 96 stars on GitHub - 1 maintainer
hypeR 2.2.0
An R Package For Geneset Enrichment Workflows3 versions - Latest release: 23 days ago - 8.49 thousand downloads total - 65 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
3 versions - Latest release: 23 days ago - 18 dependent packages - 211 thousand downloads total - 18 stars on GitHub - 1 maintainer
gdsfmt 1.40.0
R Interface to CoreArray Genomic Data Structure (GDS) Files3 versions - Latest release: 23 days ago - 18 dependent packages - 211 thousand downloads total - 18 stars on GitHub - 1 maintainer
martini 1.24.0
GWAS Incorporating Networks3 versions - Latest release: 24 days ago - 7.58 thousand downloads total - 4 stars on GitHub - 1 maintainer
vissE 1.12.0
Visualising Set Enrichment Analysis Results3 versions - Latest release: 24 days ago - 4.17 thousand downloads total - 10 stars on GitHub - 1 maintainer
doubletrouble 1.4.0
Identification and classification of duplicated genes6 versions - Latest release: 25 days ago - 1.65 thousand downloads total - 7 stars on GitHub - 1 maintainer
HIBAG 1.40.0
HLA Genotype Imputation with Attribute Bagging5 versions - Latest release: 26 days ago - 20.1 thousand downloads total - 26 stars on GitHub - 1 maintainer
cTRAP 1.22.0
Identification of candidate causal perturbations from differential gene expression data4 versions - Latest release: 26 days ago - 6.62 thousand downloads total - 5 stars on GitHub - 1 maintainer
BgeeDB 2.30.0
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities...3 versions - Latest release: about 1 month ago - 2 dependent packages - 17.4 thousand downloads total - 13 stars on GitHub - 4 maintainers
PhyloProfile 1.18.0
PhyloProfile7 versions - Latest release: about 1 month ago - 7.09 thousand downloads total - 29 stars on GitHub - 1 maintainer
MungeSumstats 1.12.0
Standardise summary statistics from GWAS4 versions - Latest release: about 1 month ago - 23 thousand downloads total - 64 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
3 versions - Latest release: about 1 month ago - 18 dependent packages - 500 thousand downloads total - 67 stars on GitHub - 1 maintainer
EBImage 4.46.0
Image processing and analysis toolbox for R3 versions - Latest release: about 1 month ago - 18 dependent packages - 500 thousand downloads total - 67 stars on GitHub - 1 maintainer
chromswitch 1.22.0 removed
An R package to detect chromatin state switches from epigenomic data1 version - Latest release: 8 months ago - 7.34 thousand downloads total - 3 stars on GitHub - 1 maintainer
Related Keywords
Software
65
r
31
bioconductor
23
Sequencing
21
GeneExpression
20
Visualization
15
DataImport
14
genomics
12
RNASeq
11
Network
11
SingleCell
10
Genetics
9
GeneSetEnrichment
9
ImmunoOncology
9
Classification
8
Transcriptomics
8
Clustering
8
Pathways
8
Preprocessing
8
Infrastructure
7
rstats
7
r-package
7
GraphAndNetwork
7
Microarray
6
StatisticalMethod
6
Coverage
6
FeatureExtraction
5
DataRepresentation
5
Normalization
5
single-cell
5
Annotation
5
DifferentialExpression
5
FunctionalGenomics
4
MultipleComparison
4
GO
4
ThirdPartyClient
4
WholeGenome
4
SystemsBiology
4
bioconductor-package
4
NetworkEnrichment
4
OneChannel
3
Metabolomics
3
SomaticMutation
3
snp
3
pathways
3
BiomedicalInformatics
3
computational-biology
3
DimensionReduction
3
scrna-seq
3
ChIPSeq
3
Reactome
3
networks
3
ComparativeGenomics
3
genomics-visualization
3
QualityControl
3
Proteomics
3
dna-methylation
3
Epigenetics
3
MethylationArray
3
KEGG
3
DNAMethylation
3
Transcription
3
Bayesian
3
rna-seq
3
BatchEffect
3
DNASeq
3
gds-format
3
tensor-decomposition
2
GenomeWideAssociation
2
transcriptomics
2
pathway-analysis
2
api-client
2
systems-biology
2
cmap
2
gene-expression
2
mRNAMicroarray
2
clustering
2
PrincipalComponent
2
data-visualization
2
Alignment
2
MethylSeq
2
CopyNumberVariation
2
SequenceMatching
2
microarray
2
Phylogenetics
2
comparative-genomics
2
GenomicVariation
2
GeneRegulation
2
cancer-genomics
2
data-science
2
tcga
2
visualization
2
DifferentialPeakCalling
2
HistoneModification
2
proteomics
2
chip-seq
2
gwas
2
microbiome
2
metagenomics
2
metabarcoding
2