Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

bioconductor.org "bioconductor" keyword

BiocPkgTools 1.20.0
Collection of simple tools for learning about Bioconductor Packages
3 versions - Latest release: 6 months ago - 13 thousand downloads total - 19 stars on GitHub - 1 maintainer
Top 4.4% on bioconductor.org
SingleR 2.6.0
Reference-Based Single-Cell RNA-Seq Annotation
4 versions - Latest release: 5 days ago - 5 dependent packages - 197 thousand downloads total - 162 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
MsCoreUtils 1.14.1
Core Utils for Mass Spectrometry Data
4 versions - Latest release: 5 months ago - 19 dependent packages - 157 thousand downloads total - 16 stars on GitHub - 1 maintainer
Top 8.6% on bioconductor.org
Spectra 1.14.0
Spectra Infrastructure for Mass Spectrometry Data
4 versions - Latest release: 14 days ago - 15 dependent packages - 47.5 thousand downloads total - 31 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
mia 1.12.0
Microbiome analysis
3 versions - Latest release: 20 days ago - 7 dependent packages - 49.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
TargetDecoy 1.8.0
Diagnostic Plots to Evaluate the Target Decoy Approach
3 versions - Latest release: 6 months ago - 2.39 thousand downloads total - 0 stars on GitHub - 1 maintainer
nullranges 1.8.0
Generation of null ranges via bootstrapping or covariate matching
3 versions - Latest release: 6 months ago - 1 dependent package - 4.44 thousand downloads total - 22 stars on GitHub - 1 maintainer
rBLAST 1.0.0
R Interface for the Basic Local Alignment Search Tool
1 version - Latest release: 21 days ago - 182 downloads total - 100 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
karyoploteR 1.30.0
Plot customizable linear genomes displaying arbitrary data
3 versions - Latest release: 18 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 stars on GitHub - 1 maintainer
dce 1.10.0
Pathway Enrichment Based on Differential Causal Effects
3 versions - Latest release: 6 months ago - 3.73 thousand downloads total - 9 stars on GitHub - 1 maintainer
Voyager 1.4.0
From geospatial to spatial omics
3 versions - Latest release: 6 months ago - 2.86 thousand downloads total - 60 stars on GitHub - 1 maintainer
segmenter 1.8.0
Perform Chromatin Segmentation Analysis in R by Calling ChromHMM
3 versions - Latest release: 6 months ago - 2.52 thousand downloads total - 3 stars on GitHub - 1 maintainer
similaRpeak 1.34.0
Metrics to estimate a level of similarity between two ChIP-Seq profiles
3 versions - Latest release: 6 months ago - 1 dependent package - 14 thousand downloads total - 7 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
MuData 1.6.0
Serialization for MultiAssayExperiment Objects
3 versions - Latest release: 6 months ago - 2.13 thousand downloads total - 4 stars on GitHub - 1 maintainer
RJMCMCNucleosomes 1.26.0
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-rea...
3 versions - Latest release: 6 months ago - 9.13 thousand downloads total - 0 stars on GitHub - 1 maintainer
MsDataHub 1.2.0
Mass Spectrometry Data on ExperimentHub
3 versions - Latest release: 6 months ago - 2 dependent packages - 1.52 thousand downloads total - 1 stars on GitHub - 1 maintainer
crisprScore 1.6.0
On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs
3 versions - Latest release: 6 months ago - 3 dependent packages - 5 thousand downloads total - 9 stars on GitHub - 1 maintainer
esATAC 1.24.0
An Easy-to-use Systematic pipeline for ATACseq data analysis
3 versions - Latest release: 6 months ago - 20.2 thousand downloads total - 22 stars on GitHub - 1 maintainer
mimager 1.26.0
mimager: The Microarray Imager
3 versions - Latest release: 6 months ago - 9.09 thousand downloads total - 0 stars on GitHub - 1 maintainer
bambu 3.4.1
Context-Aware Transcript Quantification from Long Read RNA-Seq data
4 versions - Latest release: about 1 month ago - 1 dependent package - 13 thousand downloads total - 118 stars on GitHub - 1 maintainer
sevenbridges 1.32.0
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
3 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 functionality
3 versions - Latest release: 6 months ago - 2 dependent packages - 9.48 thousand downloads total - 6 stars on GitHub - 1 maintainer
fedup 1.10.0
Fisher's Test for Enrichment and Depletion of User-Defined Pathways
3 versions - Latest release: 6 months ago - 2.96 thousand downloads total - 7 stars on GitHub - 1 maintainer
rmelting 1.18.0
R Interface to MELTING 5
3 versions - Latest release: 6 months ago - 6.43 thousand downloads total - 2 stars on GitHub - 1 maintainer
crisprBowtie 1.6.0
Bowtie-based alignment of CRISPR gRNA spacer sequences
3 versions - Latest release: 6 months ago - 2 dependent packages - 4.72 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
recount 1.30.0
Explore and download data from the recount project
3 versions - Latest release: 19 days ago - 6 dependent packages - 52.7 thousand downloads total - 40 stars on GitHub - 1 maintainer
Modstrings 1.18.0
Working with modified nucleotide sequences
3 versions - Latest release: 6 months ago - 4 dependent packages - 10.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
crisprBwa 1.6.0
BWA-based alignment of CRISPR gRNA spacer sequences
3 versions - Latest release: 6 months ago - 1 dependent package - 2.59 thousand downloads total - 1 stars on GitHub - 1 maintainer
cmapR 1.14.0
CMap Tools in R
3 versions - Latest release: 6 months ago - 21.4 thousand downloads total - 78 stars on GitHub - 1 maintainer
consensusSeekeR 1.30.0
Detection of consensus regions inside a group of experiences using genomic positions and genomic ...
3 versions - Latest release: 6 months ago - 2 dependent packages - 12.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
ramr 1.10.0
Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
3 versions - Latest release: 6 months ago - 3.04 thousand downloads total - 0 stars on GitHub - 1 maintainer
ImmuneSpaceR 1.30.0
A Thin Wrapper around the ImmuneSpace Data and Tools Portal
3 versions - Latest release: 6 months ago - 12.2 thousand downloads total - 25 stars on GitHub - 1 maintainer
DiscoRhythm 1.18.0
Interactive Workflow for Discovering Rhythmicity in Biological Data
3 versions - Latest release: 6 months ago - 6.91 thousand downloads total - 11 stars on GitHub - 1 maintainer
tidySingleCellExperiment 1.14.0
Brings SingleCellExperiment to the Tidyverse
3 versions - Latest release: 19 days ago - 4 dependent packages - 7.68 thousand downloads total - 34 stars on GitHub - 1 maintainer
crisprDesign 1.4.0
Comprehensive design of CRISPR gRNAs for nucleases and base editors
3 versions - Latest release: 6 months ago - 3 dependent packages - 4 thousand downloads total - 15 stars on GitHub - 1 maintainer
tRNA 1.20.1
Analyzing tRNA sequences and structures
4 versions - Latest release: 3 months ago - 2 dependent packages - 9.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
NormalyzerDE 1.20.0
Evaluation of normalization methods and calculation of differential expression analysis statistics
3 versions - Latest release: 6 months ago - 12.2 thousand downloads total - 18 stars on GitHub - 1 maintainer
mistyR 1.12.0
Multiview Intercellular SpaTial modeling framework
4 versions - Latest release: 7 days ago - 4.1 thousand downloads total - 39 stars on GitHub - 1 maintainer
tidybulk 1.16.0
Brings transcriptomics to the tidyverse
5 versions - Latest release: 13 days ago - 1 dependent package - 9.88 thousand downloads total - 159 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
MSnbase 2.30.1
Base Functions and Classes for Mass Spectrometry and Proteomics
4 versions - Latest release: 21 days ago - 30 dependent packages - 395 thousand downloads total - 120 stars on GitHub - 1 maintainer
signeR 2.6.0
Empirical Bayesian approach to mutational signature discovery
3 versions - Latest release: 7 days ago - 14.2 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 2.6% on bioconductor.org
biomaRt 2.60.0
Interface to BioMart databases (i.e. Ensembl)
5 versions - Latest release: 20 days ago - 124 dependent packages - 3.99 million downloads total - 31 stars on GitHub - 1 maintainer
crisprViz 1.6.0
Visualization Functions for CRISPR gRNAs
3 versions - Latest release: 7 days ago - 2 dependent packages - 3.21 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.72.0
Get data from NCBI Gene Expression Omnibus (GEO)
3 versions - Latest release: 19 days ago - 47 dependent packages - 1.87 million downloads total - 82 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.2.1
LC-MS and GC-MS Data Analysis
6 versions - Latest release: 8 days ago - 15 dependent packages - 852 thousand downloads total - 157 stars on GitHub - 1 maintainer
tRNAdbImport 1.22.0
Importing from tRNAdb and mitotRNAdb as GRanges objects
4 versions - Latest release: 9 days ago - 1 dependent package - 7.28 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
DEGreport 1.40.0
Report of DEG analysis
6 versions - Latest release: 9 days ago - 1 dependent package - 58.6 thousand downloads total - 22 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
TCGAbiolinks 2.32.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
4 versions - Latest release: 12 days ago - 7 dependent packages - 364 thousand downloads total - 274 stars on GitHub - 2 maintainers
Top 5.5% on bioconductor.org
splatter 1.26.0
Simple Simulation of Single-cell RNA Sequencing Data
2 versions - Latest release: 7 months ago - 6 dependent packages - 41.9 thousand downloads total - 205 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
ProtGenerics 1.36.0
Generic infrastructure for Bioconductor mass spectrometry packages
3 versions - Latest release: 13 days ago - 20 dependent packages - 979 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
pcaExplorer 2.30.0
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
3 versions - Latest release: 20 days ago - 2 dependent packages - 49.4 thousand downloads total - 52 stars on GitHub - 1 maintainer
Top 4.1% on bioconductor.org
GenomicDataCommons 1.28.0
NIH / NCI Genomic Data Commons Access
3 versions - Latest release: 21 days ago - 3 dependent packages - 92.3 thousand downloads total - 82 stars on GitHub - 1 maintainer
GeneTonic 2.8.0
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional ...
3 versions - Latest release: 20 days ago - 1 dependent package - 10 thousand downloads total - 75 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
ensembldb 2.28.0
Utilities to create and use Ensembl-based annotation databases
3 versions - Latest release: 20 days ago - 40 dependent packages - 1.06 million downloads total - 33 stars on GitHub - 1 maintainer
crisprBase 1.6.0
Base functions and classes for CRISPR gRNA design
2 versions - Latest release: 7 months ago - 6 dependent packages - 4.34 thousand downloads total - 2 stars on GitHub - 1 maintainer
QFeatures 1.14.1
Quantitative features for mass spectrometry data
4 versions - Latest release: 10 days ago - 6 dependent packages - 35.5 thousand downloads total - 20 stars on GitHub - 1 maintainer
scp 1.14.0
Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
3 versions - Latest release: 10 days ago - 5.67 thousand downloads total - 18 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
pRoloc 1.44.0
A unifying bioinformatics framework for spatial proteomics
3 versions - Latest release: 10 days ago - 3 dependent packages - 55.5 thousand downloads total - 14 stars on GitHub - 1 maintainer
POMA 1.14.0
Tools for Omics Data Analysis
3 versions - Latest release: 11 days ago - 1 dependent package - 4.86 thousand downloads total - 10 stars on GitHub - 1 maintainer
BiocHail 1.4.0
basilisk and hail
3 versions - Latest release: 12 days ago - 942 downloads total - 6 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
aroma.light 3.34.0
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Da...
3 versions - Latest release: 12 days ago - 3 dependent packages - 324 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
Rhdf5lib 1.26.0
hdf5 library as an R package
5 versions - Latest release: 13 days ago - 3 dependent packages - 1.85 million downloads total - 6 stars on GitHub - 1 maintainer
iSEEhex 1.6.0
iSEE extension for summarising data points in hexagonal bins
3 versions - Latest release: 13 days ago - 1 dependent package - 3.36 thousand downloads total - 0 stars on GitHub - 1 maintainer
fishpond 2.10.0
Fishpond: downstream methods and tools for expression data
3 versions - Latest release: 13 days ago - 1 dependent package - 27.1 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
rpx 2.12.0
R Interface to the ProteomeXchange Repository
3 versions - Latest release: 13 days ago - 3 dependent packages - 51.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
flowcatchR 1.38.0
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
3 versions - Latest release: 20 days ago - 15.4 thousand downloads total - 5 stars on GitHub - 1 maintainer
affxparser 1.76.0
Affymetrix File Parsing SDK
3 versions - Latest release: 20 days ago - 10 dependent packages - 323 thousand downloads total - 6 stars on GitHub - 1 maintainer
CTexploreR 1.0.0
Explores Cancer Testis Genes
1 version - Latest release: 21 days ago - 256 downloads total - 0 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
dada2 1.32.0
Accurate, high-resolution sample inference from amplicon sequencing data
3 versions - Latest release: 14 days ago - 2 dependent packages - 727 thousand downloads total - 446 stars on GitHub - 1 maintainer
psichomics 1.30.0
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
4 versions - Latest release: 15 days ago - 14.4 thousand downloads total - 33 stars on GitHub - 1 maintainer
cTRAP 1.22.0
Identification of candidate causal perturbations from differential gene expression data
4 versions - Latest release: 15 days ago - 6.62 thousand downloads total - 5 stars on GitHub - 1 maintainer
iSEEhub 1.6.0
iSEE for the Bioconductor ExperimentHub
3 versions - Latest release: 15 days ago - 2.28 thousand downloads total - 4 stars on GitHub - 1 maintainer
TnT 1.26.0
Interactive Visualization for Genomic Features
3 versions - Latest release: 17 days ago - 7.94 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 8.2% on bioconductor.org
zellkonverter 1.14.0
Conversion Between scRNA-seq Objects
4 versions - Latest release: 17 days ago - 6 dependent packages - 43.4 thousand downloads total - 132 stars on GitHub - 1 maintainer
epialleleR 1.12.0
Fast, Epiallele-Aware Methylation Caller and Reporter
3 versions - Latest release: 18 days ago - 2.98 thousand downloads total - 3 stars on GitHub - 1 maintainer
TargetSearch 2.6.0
A package for the analysis of GC-MS metabolite profiling data
4 versions - Latest release: 19 days ago - 30.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
qsvaR 1.8.0
Generate Quality Surrogate Variable Analysis for Degradation Correction
3 versions - Latest release: 19 days ago - 2.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
regutools 1.16.0
regutools: an R package for data extraction from RegulonDB
3 versions - Latest release: 19 days ago - 4.33 thousand downloads total - 4 stars on GitHub - 1 maintainer
TREG 1.8.0
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
3 versions - Latest release: 19 days ago - 1.75 thousand downloads total - 4 stars on GitHub - 1 maintainer
brainflowprobes 1.18.0
Plots and annotation for choosing BrainFlow target probe sequence
3 versions - Latest release: 19 days ago - 4.96 thousand downloads total - 0 stars on GitHub - 1 maintainer
biocthis 1.14.0
Automate package and project setup for Bioconductor packages
3 versions - Latest release: 19 days ago - 2 dependent packages - 16.4 thousand downloads total - 49 stars on GitHub - 1 maintainer
derfinderPlot 1.38.0
Plotting functions for derfinder
3 versions - Latest release: 19 days ago - 3 dependent packages - 21.4 thousand downloads total - 2 stars on GitHub - 1 maintainer
recount3 1.14.0
Explore and download data from the recount3 project
3 versions - Latest release: 19 days ago - 14.1 thousand downloads total - 27 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
derfinderHelper 1.38.0
derfinder helper package
3 versions - Latest release: 19 days ago - 1 dependent package - 59 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
derfinder 1.38.0
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via ...
3 versions - Latest release: 19 days ago - 6 dependent packages - 67.7 thousand downloads total - 42 stars on GitHub - 1 maintainer
iSEEde 1.2.0
iSEE extension for panels related to differential expression analysis
2 versions - Latest release: 20 days ago - 1 dependent package - 820 downloads total - 1 stars on GitHub - 1 maintainer
ideal 1.28.0
Interactive Differential Expression AnaLysis
3 versions - Latest release: 20 days ago - 14.5 thousand downloads total - 29 stars on GitHub - 1 maintainer
RBioFormats 1.4.0
R interface to Bio-Formats
3 versions - Latest release: 20 days ago - 1 dependent package - 2.3 thousand downloads total - 23 stars on GitHub - 1 maintainer
RNAmodR.RiboMethSeq 1.18.0
Detection of 2'-O methylations by RiboMethSeq
3 versions - Latest release: 20 days ago - 5.17 thousand downloads total - 1 stars on GitHub - 1 maintainer
RLSeq 1.6.0
RLSeq: An analysis package for R-loop mapping data
2 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 analysis
2 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 Networks
2 versions - Latest release: 6 months ago - 1 dependent package - 19.6 thousand downloads total - 2 stars on GitHub - 1 maintainer
iSEEpathways 1.0.0
iSEE extension for panels related to pathway analysis
1 version - Latest release: 7 months ago - 677 downloads total - 1 stars on GitHub - 1 maintainer
nucleoSim 1.30.0
Generate synthetic nucleosome maps
2 versions - Latest release: 7 months ago - 1 dependent package - 10.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
scPCA 1.16.0
Sparse Contrastive Principal Component Analysis
2 versions - Latest release: 6 months ago - 6.51 thousand downloads total - 10 stars on GitHub - 1 maintainer
scviR 1.2.0
experimental inferface from R to scvi-tools
2 versions - Latest release: 6 months ago - 1.01 thousand downloads total - 6 stars on GitHub - 1 maintainer
TEKRABber 1.6.0
An R package estimates the correlations of orthologs and transposable elements between two species
2 versions - Latest release: 6 months ago - 2.41 thousand downloads total - 1 stars on GitHub - 1 maintainer
Structstrings 1.18.0
Implementation of the dot bracket annotations with Biostrings
2 versions - Latest release: 6 months ago - 3 dependent packages - 8.23 thousand downloads total - 3 stars on GitHub - 1 maintainer
tRNAscanImport 1.22.0
Importing a tRNAscan-SE result file as GRanges object
2 versions - Latest release: 6 months ago - 2 dependent packages - 7.62 thousand downloads total - 2 stars on GitHub - 1 maintainer
Related Keywords
Software 119 r 62 Sequencing 36 Visualization 35 GeneExpression 31 DataImport 30 DifferentialExpression 28 ImmunoOncology 27 RNASeq 24 Infrastructure 24 bioinformatics 23 rstats 22 Coverage 15 Transcriptomics 14 Transcription 14 MassSpectrometry 13 bioconductor-package 13 QualityControl 12 MultipleComparison 12 mass-spectrometry 11 Proteomics 11 SingleCell 11 proteomics 10 Normalization 9 Pathways 9 GUI 9 GeneSetEnrichment 9 FunctionalGenomics 9 Clustering 9 Microarray 8 Preprocessing 8 Genetics 8 r-package 8 Epigenetics 8 ChIPSeq 8 Classification 7 rnaseq 7 DataRepresentation 7 StatisticalMethod 7 Alignment 7 genomics 7 Annotation 7 Metabolomics 6 ReportWriting 6 grna-sequences 6 crispr 6 grna-sequence 6 Regression 6 Network 6 CRISPR 6 grna 6 crispr-design 6 metabolomics 6 GO 6 derfinder 6 shiny 6 ShinyApps 6 OneChannel 6 crispr-target 5 package 5 PrincipalComponent 5 transcriptomics 5 DNAMethylation 5 WorkflowStep 5 rna 5 crispr-cas9 5 sgrna-design 5 deseq2 5 sgrna 5 sequences 5 BiologicalQuestion 5 GeneTarget 4 GeneRegulation 4 DifferentialPeakCalling 4 DifferentialMethylation 4 scrna-seq 4 structures 4 gene-expression 4 HistoneModification 4 user-friendly 4 rna-seq-analysis 4 MethylSeq 4 data-visualization 4 crispr-analysis 3 annotation-agnostic 3 ThirdPartyClient 3 modifications 3 BiomedicalInformatics 3 FlowCytometry 3 rna-seq 3 rnamodr 3 human 3 DNaseSeq 3 GenomeAnnotation 3 BatchEffect 3 ATACSeq 3 rna-seq-data 3 reproducible-research 3 DNASeq 3 iseeu 3