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
Top 1.4% on bioconductor.org
3 versions - Latest release: 20 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: 20 days ago - 47 dependent packages - 1.87 million downloads total - 82 stars on GitHub - 1 maintainer
BioCor 1.26.0
Functional similarities3 versions - Latest release: 6 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: 7 days ago - 2.01 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 5.6% on bioconductor.org
3 versions - Latest release: 12 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: 12 days ago - 4 dependent packages - 50.3 thousand downloads total - 48 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
3 versions - Latest release: 22 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: 22 days ago - 9 dependent packages - 226 thousand downloads total - 421 stars on GitHub - 1 maintainer
rBLAST 1.0.0
R Interface for the Basic Local Alignment Search Tool1 version - Latest release: 22 days ago - 182 downloads total - 100 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
3 versions - Latest release: 20 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: 20 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 months ago - 4.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
cmapR 1.14.0
CMap Tools in R3 versions - Latest release: 6 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: 6 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: 6 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: 7 days ago - 901 downloads total - 2 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
7 versions - Latest release: 8 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: 8 days ago - 11 dependent packages - 86.6 thousand downloads total - 42 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
4 versions - Latest release: 22 days ago - 30 dependent packages - 395 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: 22 days ago - 30 dependent packages - 395 thousand downloads total - 120 stars on GitHub - 1 maintainer
netSmooth 1.24.0
Network smoothing for scRNAseq3 versions - Latest release: 9 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: 9 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: 10 days ago - 5 dependent packages - 56.6 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
2 versions - Latest release: 7 months ago - 6 dependent packages - 41.9 thousand downloads total - 205 stars on GitHub - 1 maintainer
splatter 1.26.0
Simple Simulation of Single-cell RNA Sequencing Data2 versions - Latest release: 7 months ago - 6 dependent packages - 41.9 thousand downloads total - 205 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
2 versions - Latest release: 6 months ago - 11 dependent packages - 229 thousand downloads total - 5 stars on GitHub - 1 maintainer
graphite 1.48.0
GRAPH Interaction from pathway Topological Environment2 versions - Latest release: 6 months ago - 11 dependent packages - 229 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 4.1% on bioconductor.org
3 versions - Latest release: 22 days 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: 22 days 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: 11 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: 12 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: 12 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: 12 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: 13 days ago - 8.49 thousand downloads total - 65 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
3 versions - Latest release: 13 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: 13 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: 15 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: 15 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: 15 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: 16 days ago - 20.1 thousand downloads total - 26 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
3 versions - Latest release: 16 days ago - 2 dependent packages - 727 thousand downloads total - 446 stars on GitHub - 1 maintainer
dada2 1.32.0
Accurate, high-resolution sample inference from amplicon sequencing data3 versions - Latest release: 16 days ago - 2 dependent packages - 727 thousand downloads total - 446 stars on GitHub - 1 maintainer
cTRAP 1.22.0
Identification of candidate causal perturbations from differential gene expression data4 versions - Latest release: 16 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: 21 days ago - 2 dependent packages - 17.4 thousand downloads total - 13 stars on GitHub - 4 maintainers
PhyloProfile 1.18.0
PhyloProfile7 versions - Latest release: 21 days ago - 7.09 thousand downloads total - 29 stars on GitHub - 1 maintainer
MungeSumstats 1.12.0
Standardise summary statistics from GWAS4 versions - Latest release: 21 days ago - 23 thousand downloads total - 64 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
3 versions - Latest release: 22 days 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: 22 days ago - 18 dependent packages - 500 thousand downloads total - 67 stars on GitHub - 1 maintainer
sparrow 1.10.0
Take command of set enrichment analyses through a unified interface3 versions - Latest release: 22 days ago - 1 dependent package - 4.19 thousand downloads total - 20 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
RLSeq 1.6.0
RLSeq: An analysis package for R-loop mapping data2 versions - Latest release: 7 months ago - 2.28 thousand downloads total - 2 stars on GitHub - 1 maintainer
cogena 1.36.0
co-expressed gene-set enrichment analysis2 versions - Latest release: 6 months ago - 17.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
rTRM 1.40.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks2 versions - Latest release: 6 months ago - 1 dependent package - 19.6 thousand downloads total - 2 stars on GitHub - 1 maintainer
getDEE2 1.12.0
Programmatic access to the DEE2 RNA expression dataset2 versions - Latest release: 6 months ago - 3.69 thousand downloads total - 4 stars on GitHub - 1 maintainer
geneXtendeR 1.28.0
Optimized Functional Annotation Of ChIP-seq Data2 versions - Latest release: 6 months ago - 13.1 thousand downloads total - 9 stars on GitHub - 1 maintainer
biobtreeR 1.14.0
Using biobtree tool from R2 versions - Latest release: 6 months ago - 4.9 thousand downloads total - 3 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...2 versions - Latest release: 6 months ago - 1.77 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
2 versions - Latest release: 6 months ago - 3 dependent packages - 63.3 thousand downloads total - 37 stars on GitHub - 1 maintainer
singscore 1.22.0
Rank-based single-sample gene set scoring method2 versions - Latest release: 6 months ago - 3 dependent packages - 63.3 thousand downloads total - 37 stars on GitHub - 1 maintainer
decontam 1.22.0
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data2 versions - Latest release: 6 months ago - 1 dependent package - 56.6 thousand downloads total - 131 stars on GitHub - 1 maintainer
ontoProc 1.24.0
processing of ontologies of anatomy, cell lines, and so on2 versions - Latest release: 7 months ago - 3 dependent packages - 13.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.22.0
Random walk with restart on multiplex and heterogeneous Networks2 versions - Latest release: 6 months ago - 1 dependent package - 9.31 thousand downloads total - 17 stars on GitHub - 1 maintainer
CiteFuse 1.14.0
CiteFuse: multi-modal analysis of CITE-seq data2 versions - Latest release: 6 months ago - 1 dependent package - 6.48 thousand downloads total - 25 stars on GitHub - 1 maintainer
scruff 1.20.0
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)2 versions - Latest release: 6 months ago - 7.41 thousand downloads total - 8 stars on GitHub - 1 maintainer
CellBench 1.18.0
Construct Benchmarks for Single Cell Analysis Methods2 versions - Latest release: 6 months ago - 2 dependent packages - 8.66 thousand downloads total - 28 stars on GitHub - 1 maintainer
orthogene 1.8.0
Interspecies gene mapping2 versions - Latest release: 7 months ago - 1 dependent package - 9.63 thousand downloads total - 33 stars on GitHub - 1 maintainer
chromswitch 1.22.0 removed
An R package to detect chromatin state switches from epigenomic data1 version - Latest release: 7 months ago - 7.34 thousand downloads total - 3 stars on GitHub - 1 maintainer
Related Keywords
Software
64
r
30
bioconductor
23
Sequencing
21
GeneExpression
20
Visualization
15
DataImport
14
genomics
12
RNASeq
10
Network
10
SingleCell
10
ImmunoOncology
9
Genetics
9
Transcriptomics
8
Clustering
8
GeneSetEnrichment
8
Classification
8
Preprocessing
8
r-package
7
Infrastructure
7
GraphAndNetwork
7
rstats
7
Pathways
7
StatisticalMethod
6
Coverage
6
Microarray
6
FeatureExtraction
5
DataRepresentation
5
Annotation
5
DifferentialExpression
5
Normalization
5
single-cell
5
FunctionalGenomics
4
SystemsBiology
4
GO
4
ThirdPartyClient
4
MultipleComparison
4
bioconductor-package
4
WholeGenome
4
NetworkEnrichment
3
BiomedicalInformatics
3
rna-seq
3
ChIPSeq
3
scrna-seq
3
DimensionReduction
3
SomaticMutation
3
ComparativeGenomics
3
OneChannel
3
genomics-visualization
3
pathways
3
Metabolomics
3
BatchEffect
3
Bayesian
3
computational-biology
3
Proteomics
3
gds-format
3
Transcription
3
snp
3
DNAMethylation
3
MethylationArray
3
QualityControl
3
dna-methylation
3
KEGG
3
DNASeq
3
Epigenetics
3
pathway-analysis
2
chip-seq
2
GenomicVariation
2
data-science
2
api-client
2
HistoneModification
2
microbiome
2
GeneRegulation
2
DifferentialPeakCalling
2
metagenomics
2
Metagenomics
2
Microbiome
2
amplicon
2
tensor-decomposition
2
metabarcoding
2
mRNAMicroarray
2
cmap
2
transcriptomics
2
microarray
2
GenomeWideAssociation
2
SNP
2
PrincipalComponent
2
gwas
2
cancer-genomics
2
proteomics
2
tcga
2
Alignment
2
SequenceMatching
2
CopyNumberVariation
2
MethylSeq
2
data-visualization
2
systems-biology
2
Phylogenetics
2
gene-expression
2
comparative-genomics
2