Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "bioconductor-package" keyword
structToolbox 1.16.0
Data processing & analysis tools for Metabolomics and other omics3 versions - Latest release: about 1 month ago - 1 dependent package - 6.45 thousand downloads total - 8 stars on GitHub - 1 maintainer
TENxIO 1.5.4
Import methods for 10X Genomics files4 versions - Latest release: about 1 month ago - 1 dependent package - 1.75 thousand downloads total - 0 stars on GitHub - 1 maintainer
VisiumIO 1.0.0
Import Visium data from the 10X Space Ranger pipeline1 version - Latest release: about 1 month ago - 357 downloads total - 0 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
4 versions - Latest release: 24 days ago - 15 dependent packages - 934 thousand downloads total - 4 stars on GitHub - 1 maintainer
beachmat 2.20.0
Compiling Bioconductor to Handle Each Matrix Type4 versions - Latest release: 24 days ago - 15 dependent packages - 934 thousand downloads total - 4 stars on GitHub - 1 maintainer
QUBIC 1.30.0
An R package for qualitative biclustering in support of gene co-expression analyses3 versions - Latest release: 6 months ago - 2 dependent packages - 25.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
crisprBase 1.6.0
Base functions and classes for CRISPR gRNA design3 versions - Latest release: 7 months ago - 6 dependent packages - 4.81 thousand downloads total - 2 stars on GitHub - 1 maintainer
BEclear 2.18.0
Correction of batch effects in DNA methylation data3 versions - Latest release: 7 months ago - 15.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 1.1% on bioconductor.org
3 versions - Latest release: about 1 month ago - 377 dependent packages - 5.57 million downloads total - 63 stars on GitHub - 1 maintainer
BiocParallel 1.38.0
Bioconductor facilities for parallel evaluation3 versions - Latest release: about 1 month ago - 377 dependent packages - 5.57 million downloads total - 63 stars on GitHub - 1 maintainer
HDTD 1.36.0
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Trans...3 versions - Latest release: 6 months ago - 13.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
GOexpress 1.36.0
Visualise microarray and RNAseq data using gene ontology annotations3 versions - Latest release: 6 months ago - 1 dependent package - 24.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 7.3% on bioconductor.org
4 versions - Latest release: 5 months ago - 7 dependent packages - 60.8 thousand downloads total - 19 stars on GitHub - 1 maintainer
TCGAutils 1.22.2
TCGA utility functions for data management4 versions - Latest release: 5 months ago - 7 dependent packages - 60.8 thousand downloads total - 19 stars on GitHub - 1 maintainer
scmeth 1.22.0
Functions to conduct quality control analysis in methylation data3 versions - Latest release: 6 months ago - 1 dependent package - 8.27 thousand downloads total - 0 stars on GitHub - 1 maintainer
EpiCompare 1.6.7
Comparison, Benchmarking & QC of Epigenomic Datasets9 versions - Latest release: about 2 months ago - 2.13 thousand downloads total - 12 stars on GitHub - 1 maintainer
DNAfusion 1.4.0
Identification of gene fusions using paired-end sequencing3 versions - Latest release: 6 months ago - 1.7 thousand downloads total - 3 stars on GitHub - 1 maintainer
pram 1.18.0
Pooling RNA-seq datasets for assembling transcript models3 versions - Latest release: 7 months ago - 5.49 thousand downloads total - 1 stars on GitHub - 1 maintainer
BASiCS 2.14.0
Bayesian Analysis of Single-Cell Sequencing data3 versions - Latest release: 6 months ago - 2 dependent packages - 17.3 thousand downloads total - 83 stars on GitHub - 1 maintainer
cellmigRation 1.10.0
Track Cells, Analyze Cell Trajectories and Compute Migration Statistics3 versions - Latest release: 7 months ago - 3.06 thousand downloads total - 0 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
Top 9.3% on bioconductor.org
3 versions - Latest release: about 1 month ago - 28 dependent packages - 702 thousand downloads total - 6 stars on GitHub - 1 maintainer
BiocSingular 1.20.0
Singular Value Decomposition for Bioconductor Packages3 versions - Latest release: about 1 month ago - 28 dependent packages - 702 thousand downloads total - 6 stars on GitHub - 1 maintainer
deconvR 1.8.0
Simulation and Deconvolution of Omic Profiles3 versions - Latest release: 7 months ago - 3.22 thousand downloads total - 9 stars on GitHub - 1 maintainer
doppelgangR 1.30.0
Identify likely duplicate samples from genomic or meta-data3 versions - Latest release: 7 months ago - 12.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
similaRpeak 1.34.0
Metrics to estimate a level of similarity between two ChIP-Seq profiles3 versions - Latest release: 7 months ago - 1 dependent package - 14 thousand downloads total - 7 stars on GitHub - 1 maintainer
crisprScore 1.6.0
On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs3 versions - Latest release: 7 months ago - 3 dependent packages - 5 thousand downloads total - 9 stars on GitHub - 1 maintainer
BridgeDbR 2.12.0
Code for using BridgeDb identifier mapping framework from within R3 versions - Latest release: 7 months ago - 18 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 6.6% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 41.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
Organism.dplyr 1.30.1
dplyr-based Access to Bioconductor Annotation Resources3 versions - Latest release: 7 months ago - 1 dependent package - 41.2 thousand downloads total - 3 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
BindingSiteFinder 2.0.0
Binding site defintion based on iCLIP data3 versions - Latest release: 7 months ago - 2.89 thousand downloads total - 3 stars on GitHub - 1 maintainer
crisprBowtie 1.6.0
Bowtie-based alignment of CRISPR gRNA spacer sequences3 versions - Latest release: 7 months ago - 2 dependent packages - 4.72 thousand downloads total - 1 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
crisprBwa 1.6.0
BWA-based alignment of CRISPR gRNA spacer sequences3 versions - Latest release: 7 months ago - 1 dependent package - 2.59 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
3 versions - Latest release: 7 months ago - 27.2 thousand downloads total - 86 stars on GitHub - 1 maintainer
scmap 1.24.0
A tool for unsupervised projection of single cell RNA-seq data3 versions - Latest release: 7 months ago - 27.2 thousand downloads total - 86 stars on GitHub - 1 maintainer
GenomicSuperSignature 1.10.0
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases3 versions - Latest release: 7 months ago - 3.29 thousand downloads total - 12 stars on GitHub - 1 maintainer
CNVRanger 1.18.1
Summarization and expression/phenotype association of CNV ranges4 versions - Latest release: 2 months ago - 8.7 thousand downloads total - 4 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
crisprViz 1.6.0
Visualization Functions for CRISPR gRNAs3 versions - Latest release: 18 days ago - 2 dependent packages - 3.21 thousand downloads total - 4 stars on GitHub - 1 maintainer
raer 1.2.0
RNA editing tools in R3 versions - Latest release: 19 days ago - 823 downloads total - 6 stars on GitHub - 1 maintainer
cBioPortalData 2.16.0
Exposes and Makes Available Data from the cBioPortal Web Resources4 versions - Latest release: 20 days ago - 4 dependent packages - 20.2 thousand downloads total - 29 stars on GitHub - 1 maintainer
UniProt.ws 2.44.0
R Interface to UniProt Web Services3 versions - Latest release: about 1 month ago - 6 dependent packages - 54.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
lefser 1.14.0
R implementation of the LEfSE method for microbiome biomarker discovery4 versions - Latest release: about 1 month ago - 1 dependent package - 16.8 thousand downloads total - 31 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: about 1 month ago - 1 dependent package - 10 thousand downloads total - 75 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
3 versions - Latest release: about 1 month ago - 1,298 dependent packages - 736 thousand downloads total - 12 stars on GitHub - 1 maintainer
BiocStyle 2.32.0
Standard styles for vignettes and other Bioconductor documents3 versions - Latest release: about 1 month ago - 1,298 dependent packages - 736 thousand downloads total - 12 stars on GitHub - 1 maintainer
PureCN 2.10.0
Copy number calling and SNV classification using targeted short read sequencing4 versions - Latest release: 23 days ago - 25.8 thousand downloads total - 120 stars on GitHub - 1 maintainer
Top 4.4% on bioconductor.org
3 versions - Latest release: 23 days ago - 4 dependent packages - 63.4 thousand downloads total - 115 stars on GitHub - 1 maintainer
SC3 1.32.0
Single-Cell Consensus Clustering3 versions - Latest release: 23 days ago - 4 dependent packages - 63.4 thousand downloads total - 115 stars on GitHub - 1 maintainer
msPurity 1.30.0
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabol...3 versions - Latest release: 25 days ago - 12.4 thousand downloads total - 15 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
4 versions - Latest release: about 1 month ago - 6 dependent packages - 225 thousand downloads total - 8 stars on GitHub - 1 maintainer
BiocCheck 1.40.0
Bioconductor-specific package checks4 versions - Latest release: about 1 month ago - 6 dependent packages - 225 thousand downloads total - 8 stars on GitHub - 1 maintainer
iSEEhub 1.6.0
iSEE for the Bioconductor ExperimentHub3 versions - Latest release: 26 days ago - 2.28 thousand downloads total - 4 stars on GitHub - 1 maintainer
terraTCGAdata 1.8.0
OpenAccess TCGA Data on Terra as MultiAssayExperiment3 versions - Latest release: about 1 month ago - 1.7 thousand downloads total - 0 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
bugsigdbr 1.10.0
R-side access to published microbial signatures from BugSigDB6 versions - Latest release: about 1 month ago - 4.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
GSEABenchmarkeR 1.24.0
Reproducible GSEA Benchmarking3 versions - Latest release: about 1 month ago - 2 dependent packages - 9.26 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 8.6% on bioconductor.org
3 versions - Latest release: about 1 month ago - 19 dependent packages - 815 thousand downloads total - 4 stars on GitHub - 1 maintainer
AnnotationFilter 1.28.0
Facilities for Filtering Bioconductor Annotation Resources3 versions - Latest release: about 1 month ago - 19 dependent packages - 815 thousand downloads total - 4 stars on GitHub - 1 maintainer
Related Keywords
Software
51
GeneExpression
13
Sequencing
13
bioconductor
13
RNASeq
11
DataImport
11
DifferentialExpression
10
r
10
SingleCell
10
Infrastructure
9
ImmunoOncology
8
FunctionalGenomics
8
Transcriptomics
8
r-package
7
Annotation
7
Visualization
7
grna
6
crispr-design
6
crispr
6
grna-sequence
6
grna-sequences
6
Preprocessing
6
CRISPR
6
Genetics
6
Microarray
6
sgrna-design
5
core-package
5
sgrna
5
crispr-target
5
crispr-cas9
5
genomics
5
DataRepresentation
5
StatisticalMethod
5
MultipleComparison
5
human-cell-atlas
4
Clustering
4
Coverage
4
Pathways
4
Transcription
4
bioinformatics
4
GeneSetEnrichment
4
GO
3
crispr-analysis
3
QualityControl
3
Classification
3
single-cell-rna-seq
3
Alignment
3
Metabolomics
3
CopyNumberVariation
3
DNAMethylation
3
ComparativeGenomics
2
Microbiome
2
lc-ms
2
SupportVectorMachine
2
ChIPSeq
2
GUI
2
dims
2
PrincipalComponent
2
DimensionReduction
2
WorkflowStep
2
GenomeAnnotation
2
ReportWriting
2
genetics
2
genes
2
GenomeWideAssociation
2
BiologicalQuestion
2
ShinyApps
2
methylation
2
aligner
2
dna-methylation
2
gene-expression
2
rpackage
2
rna-seq-analysis
2
Network
2
CellBiology
2
statistics
2
GeneTarget
2
SNP
2
metabolomics
2
FeatureExtraction
2
GenomicVariation
2
shiny
2
genomics-analysis
1
tumor-heterogeneity
1
rna-binding-proteins
1
iclip
1
binding-sites
1
binding-site-classification
1
GeneRegulation
1
bowtie
1
rstats
1
MethylationArray
1
tensor-decomposition
1
bwa
1
genomics-visualization
1
projection-mapping
1
SystemsBiology
1
exploratory-data-analysis
1
gsea
1
mesh
1