Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org packages
Loading...
OSAT 1.50.0
OSAT: Optimal Sample Assignment Tool3 versions - Latest release: 6 months ago - 21.7 thousand downloads total - 1 maintainer
switchBox 1.38.0
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair ...3 versions - Latest release: 6 months ago - 1 dependent package - 18.3 thousand downloads total - 3 maintainers
shinyepico 1.10.0
ShinyÉPICo3 versions - Latest release: 6 months ago - 3.54 thousand downloads total - 3 stars on GitHub - 1 maintainer
Guitar 2.18.0
Guitar3 versions - Latest release: 6 months ago - 18.4 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
3 versions - Latest release: 20 days ago - 7 dependent packages - 49.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
mia 1.12.0
Microbiome analysis3 versions - Latest release: 20 days ago - 7 dependent packages - 49.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
SynMut 1.18.0
SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures3 versions - Latest release: 6 months ago - 5.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
midasHLA 1.10.0
R package for immunogenomics data handling and association analysis3 versions - Latest release: 6 months ago - 5.76 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 42 thousand downloads total - 1 maintainer
clusterStab 1.74.0
Compute cluster stability scores for microarray data3 versions - Latest release: 6 months ago - 42 thousand downloads total - 1 maintainer
MethylAid 1.36.0
Visual and interactive quality control of large Illumina DNA Methylation array data sets3 versions - Latest release: 6 months ago - 18.5 thousand downloads total - 1 maintainer
GGPA 1.14.0
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architec...3 versions - Latest release: 6 months ago - 4.23 thousand downloads total - 1 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
spqn 1.14.0
Spatial quantile normalization3 versions - Latest release: 6 months ago - 4.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
anota2seq 1.24.0
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq3 versions - Latest release: 6 months ago - 11.1 thousand downloads total - 2 maintainers
Top 8.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 1 maintainer
maigesPack 1.66.0
Functions to handle cDNA microarray data, including several methods of data analysis3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 1 maintainer
MetaNeighbor 1.22.0
Single cell replicability analysis3 versions - Latest release: 6 months ago - 10 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
3 versions - Latest release: 6 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: 6 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: 6 months ago - 1 dependent package - 22.4 thousand downloads total - 1 maintainer
odseq 1.30.0
Outlier detection in multiple sequence alignments3 versions - Latest release: 6 months ago - 10.8 thousand downloads total - 1 maintainer
doppelgangR 1.30.0
Identify likely duplicate samples from genomic or meta-data3 versions - Latest release: 6 months ago - 12.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
TargetDecoy 1.8.0
Diagnostic Plots to Evaluate the Target Decoy Approach3 versions - Latest release: 6 months ago - 2.39 thousand downloads total - 0 stars on GitHub - 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
Top 8.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 2 dependent packages - 31 thousand downloads total - 1 maintainer
OLIN 1.80.0
Optimized local intensity-dependent normalisation of two-color microarrays3 versions - Latest release: 6 months ago - 2 dependent packages - 31 thousand downloads total - 1 maintainer
sechm 1.10.0
sechm: Complex Heatmaps from a SummarizedExperiment3 versions - Latest release: 6 months ago - 1 dependent package - 5.31 thousand downloads total - 4 stars on GitHub - 1 maintainer
barcodetrackR 1.10.0
Functions for Analyzing Cellular Barcoding Data3 versions - Latest release: 6 months ago - 3.6 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 9.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 29.5 thousand downloads total - 1 maintainer
HEM 1.74.0
Heterogeneous error model for identification of differentially expressed genes under multiple con...3 versions - Latest release: 6 months ago - 29.5 thousand downloads total - 1 maintainer
Top 7.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 34.1 thousand downloads total - 1 maintainer
plgem 1.74.0
Detect differential expression in microarray and proteomics datasets with the Power Law Global Er...3 versions - Latest release: 6 months ago - 1 dependent package - 34.1 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
MineICA 1.42.0
Analysis of an ICA decomposition obtained on genomics data3 versions - Latest release: 6 months ago - 21.5 thousand downloads total - 1 maintainer
ChIPXpress 1.46.0
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip ...3 versions - Latest release: 6 months ago - 16.7 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 40.5 thousand downloads total - 1 maintainer
girafe 1.54.0
Genome Intervals and Read Alignments for Functional Exploration3 versions - Latest release: 6 months ago - 40.5 thousand downloads total - 1 maintainer
megadepth 1.12.0
megadepth: BigWig and BAM related utilities3 versions - Latest release: 6 months ago - 2 dependent packages - 6.86 thousand downloads total - 11 stars on GitHub - 1 maintainer
epigraHMM 1.10.0
Epigenomic R-based analysis with hidden Markov models3 versions - Latest release: 6 months ago - 3.3 thousand downloads total - 1 maintainer
tenXplore 1.24.0
ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics3 versions - Latest release: 6 months ago - 8.35 thousand downloads total - 1 maintainer
Top 8.0% on bioconductor.org
4 versions - Latest release: 3 months ago - 5 dependent packages - 65.6 thousand downloads total - 1 maintainer
TrajectoryUtils 1.10.1
Single-Cell Trajectory Analysis Utilities4 versions - Latest release: 3 months ago - 5 dependent packages - 65.6 thousand downloads total - 1 maintainer
easier 1.8.0
Estimate Systems Immune Response from RNA-seq data3 versions - Latest release: 6 months ago - 4.36 thousand downloads total - 1 maintainer
Top 7.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 37.4 thousand downloads total - 1 maintainer
CGEN 3.38.0
An R package for analysis of case-control studies in genetic epidemiology3 versions - Latest release: 6 months ago - 37.4 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
2 versions - Latest release: 6 months ago - 31.2 thousand downloads total - 1 maintainer
gaggle 1.70.0 removed
Broadcast data between R and Gaggle2 versions - Latest release: 6 months ago - 31.2 thousand downloads total - 1 maintainer
metabomxtr 1.36.0
A package to run mixture models for truncated metabolomics data with normal or lognormal distribu...3 versions - Latest release: 6 months ago - 15 thousand downloads total - 1 maintainer
COMPASS 1.40.0
Combinatorial Polyfunctionality Analysis of Single Cells3 versions - Latest release: 6 months ago - 20 thousand downloads total - 6 stars on GitHub - 1 maintainer
QSutils 1.20.0
Quasispecies Diversity3 versions - Latest release: 6 months ago - 19.7 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 33.5 thousand downloads total - 1 maintainer
CoCiteStats 1.74.0
Different test statistics based on co-citation.3 versions - Latest release: 6 months ago - 33.5 thousand downloads total - 1 maintainer
SPEM 1.42.0
S-system parameter estimation method3 versions - Latest release: 6 months ago - 1 dependent package - 19.8 thousand downloads total - 1 maintainer
HPAStainR 1.12.0 removed
Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes2 versions - Latest release: 6 months ago - 2.37 thousand downloads total - 2 stars on GitHub - 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
CuratedAtlasQueryR 1.2.0
Queries the Human Cell Atlas3 versions - Latest release: 15 days ago - 1.07 thousand downloads total - 77 stars on GitHub - 1 maintainer
IMPCdata 1.38.0
Retrieves data from IMPC database3 versions - Latest release: 6 months ago - 12.8 thousand downloads total - 1 maintainer
phantasus 1.22.2
Visual and interactive gene expression analysis3 versions - Latest release: 6 months ago - 11 thousand downloads total - 1 maintainer
ISoLDE 1.30.0
Integrative Statistics of alleLe Dependent Expression3 versions - Latest release: 6 months ago - 9.18 thousand downloads total - 1 maintainer
dagLogo 1.40.0
dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups b...3 versions - Latest release: 6 months ago - 18.8 thousand downloads total - 1 maintainer
SpacePAC 1.40.0
Identification of Mutational Clusters in 3D Protein Space via Simulation.3 versions - Latest release: 6 months ago - 1 dependent package - 18.2 thousand downloads total - 1 maintainer
tigre 1.56.0
Transcription factor Inference through Gaussian process Reconstruction of Expression3 versions - Latest release: 6 months ago - 26.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
RNAmodR.ML 1.16.0
Detecting patterns of post-transcriptional modifications using machine learning3 versions - Latest release: 6 months ago - 5.02 thousand downloads total - 0 stars on GitHub - 1 maintainer
Scale4C 1.24.0
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data3 versions - Latest release: 6 months ago - 7.48 thousand downloads total - 1 maintainer
pathVar 1.32.0
Methods to Find Pathways with Significantly Different Variability3 versions - Latest release: 6 months ago - 9.78 thousand downloads total - 1 maintainer
MQmetrics 1.10.0
Quality Control of Protemics Data3 versions - Latest release: 6 months ago - 2.66 thousand downloads total - 1 maintainer
PanViz 1.4.0
Integrating Multi-Omic Network Data With Summay-Level GWAS Data3 versions - Latest release: 6 months ago - 1.66 thousand downloads total - 3 stars on GitHub - 1 maintainer
wpm 1.12.0
Well Plate Maker3 versions - Latest release: 6 months ago - 4 thousand downloads total - 5 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
TOAST 1.16.0
Tools for the analysis of heterogeneous tissues3 versions - Latest release: 6 months ago - 3 dependent packages - 15.7 thousand downloads total - 8 stars on GitHub - 1 maintainer
synapsis 1.8.0
An R package to automate the analysis of double-strand break repair during meiosis3 versions - Latest release: 6 months ago - 2.18 thousand downloads total - 1 maintainer
Top 7.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 22.4 thousand downloads total - 87 stars on GitHub - 1 maintainer
TitanCNA 1.40.0
Subclonal copy number and LOH prediction from whole genome sequencing of tumours3 versions - Latest release: 6 months ago - 22.4 thousand downloads total - 87 stars on GitHub - 1 maintainer
SICtools 1.32.0
Find SNV/Indel differences between two bam files with near relationship3 versions - Latest release: 6 months ago - 9.24 thousand downloads total - 1 maintainer
svaNUMT 1.8.0
NUMT detection from structural variant calls3 versions - Latest release: 6 months ago - 2.46 thousand downloads total - 3 stars on GitHub - 1 maintainer
anota 1.50.0
ANalysis Of Translational Activity (ANOTA).3 versions - Latest release: 6 months ago - 1 dependent package - 29.3 thousand downloads total - 1 maintainer
PSEA 1.36.0
Population-Specific Expression Analysis.3 versions - Latest release: 6 months ago - 13.8 thousand downloads total - 1 maintainer
dcGSA 1.30.0
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles3 versions - Latest release: 6 months ago - 10.5 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 2 dependent packages - 39.6 thousand downloads total - 1 maintainer
GeneMeta 1.74.0
MetaAnalysis for High Throughput Experiments3 versions - Latest release: 6 months ago - 2 dependent packages - 39.6 thousand downloads total - 1 maintainer
netboost 2.10.0
Network Analysis Supported by Boosting3 versions - Latest release: 6 months ago - 4.72 thousand downloads total - 1 maintainer
scMultiSim 1.0.0
Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell In...1 version - Latest release: 21 days ago - 144 downloads total - 18 stars on GitHub - 1 maintainer
cydar 1.26.0
Using Mass Cytometry for Differential Abundance Analyses3 versions - Latest release: 6 months ago - 13.2 thousand downloads total - 1 maintainer
methylMnM 1.40.0
detect different methylation level (DMR)3 versions - Latest release: 6 months ago - 1 dependent package - 17.6 thousand downloads total
surfaltr 1.8.0
Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr3 versions - Latest release: 6 months ago - 2.28 thousand downloads total - 1 maintainer
oncomix 1.24.0
Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data3 versions - Latest release: 6 months ago - 7.63 thousand downloads total - 1 maintainer
BaalChIP 1.28.0
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes3 versions - Latest release: 6 months ago - 11.7 thousand downloads total - 1 maintainer
adductomicsR 1.18.0
Processing of adductomic mass spectral datasets3 versions - Latest release: 6 months ago - 6.85 thousand downloads total - 1 stars on GitHub - 1 maintainer
powerTCR 1.22.0
Model-Based Comparative Analysis of the TCR Repertoire3 versions - Latest release: 6 months ago - 1 dependent package - 26.9 thousand downloads total - 1 maintainer
CNVrd2 1.40.0
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from...3 versions - Latest release: 6 months ago - 22.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
scDD 1.26.0
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions3 versions - Latest release: 6 months ago - 1 dependent package - 19.2 thousand downloads total - 32 stars on GitHub - 1 maintainer
ADaCGH2 2.42.0
Analysis of big data from aCGH experiments using parallel computing and ff objects3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
epigenomix 1.42.0
Epigenetic and gene transcription data normalization and integration with mixture models3 versions - Latest release: 6 months ago - 20.6 thousand downloads total - 1 maintainer
Top 7.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 33.1 thousand downloads total - 1 maintainer
miRNApath 1.62.0
miRNApath: Pathway Enrichment for miRNA Expression Data3 versions - Latest release: 6 months ago - 33.1 thousand downloads total - 1 maintainer
iPath 1.8.0
iPath pipeline for detecting perturbed pathways at individual level3 versions - Latest release: 6 months ago - 2.34 thousand downloads total - 2 stars on GitHub - 1 maintainer
BSgenomeForge 1.2.3
Forge BSgenome data packages5 versions - Latest release: about 1 month ago - 1 dependent package - 8.28 thousand downloads total - 1 maintainer
rBLAST 1.0.0
R Interface for the Basic Local Alignment Search Tool1 version - Latest release: 21 days ago - 182 downloads total - 100 stars on GitHub - 1 maintainer
lute 1.0.0
Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments1 version - Latest release: 21 days ago - 340 downloads total - 2 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
3 versions - Latest release: 13 days ago - 6 dependent packages - 123 thousand downloads total - 0 stars on GitHub - 1 maintainer
baySeq 2.38.0
Empirical Bayesian analysis of patterns of differential expression in count data3 versions - Latest release: 13 days ago - 6 dependent packages - 123 thousand downloads total - 0 stars on GitHub - 1 maintainer
pipeFrame 1.18.0
Pipeline framework for bioinformatics in R3 versions - Latest release: 6 months ago - 2 dependent packages - 10.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
3 versions - Latest release: 18 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: 18 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 stars on GitHub - 1 maintainer
BatchQC 1.30.0
Batch Effects Quality Control Software3 versions - Latest release: 6 months ago - 20.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 1.1% on bioconductor.org
3 versions - Latest release: 20 days ago - 377 dependent packages - 5.55 million downloads total - 63 stars on GitHub - 1 maintainer
BiocParallel 1.38.0
Bioconductor facilities for parallel evaluation3 versions - Latest release: 20 days ago - 377 dependent packages - 5.55 million downloads total - 63 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 63.4 thousand downloads total - 1 maintainer
BioNet 1.62.0
Routines for the functional analysis of biological networks3 versions - Latest release: 6 months ago - 3 dependent packages - 63.4 thousand downloads total - 1 maintainer
HiCBricks 1.20.0
Framework for Storing and Accessing Hi-C Data Through HDF Files3 versions - Latest release: 6 months ago - 1 dependent package - 8.09 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 34.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
segmentSeq 2.36.0
Methods for identifying small RNA loci from high-throughput sequencing data3 versions - Latest release: 6 months ago - 34.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
IRISFGM 1.10.0
Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq3 versions - Latest release: 6 months ago - 3 thousand downloads total - 1 maintainer
BiFET 1.22.0
Bias-free Footprint Enrichment Test3 versions - Latest release: 6 months ago - 8.91 thousand downloads total - 1 maintainer
randPack 1.48.0
Randomization routines for Clinical Trials3 versions - Latest release: 6 months ago - 21.9 thousand downloads total - 1 maintainer
omicsPrint 1.22.0
Cross omic genetic fingerprinting3 versions - Latest release: 6 months ago - 7.42 thousand downloads total - 1 maintainer
Top 7.4% on bioconductor.org
3 versions - Latest release: 6 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: 6 months ago - 38 thousand downloads total - 1 maintainer
cosmiq 1.36.0
cosmiq - COmbining Single Masses Into Quantities3 versions - Latest release: 6 months ago - 15.9 thousand downloads total - 1 maintainer
dce 1.10.0
Pathway Enrichment Based on Differential Causal Effects3 versions - Latest release: 6 months ago - 3.73 thousand downloads total - 9 stars on GitHub - 1 maintainer