Ecosyste.ms: Packages

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bioconductor.org packages

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ScaledMatrix 1.10.0
Creating a DelayedMatrix of Scaled and Centered Values
2 versions - Latest release: 4 months ago - 5 dependent packages - 457 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
maftools 2.18.0
Summarize, Analyze and Visualize MAF Files
2 versions - Latest release: 4 months ago - 8 dependent packages - 215 thousand downloads total - 407 stars on GitHub - 1 maintainer
ompBAM 1.6.0
C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files
2 versions - Latest release: 3 months ago - 1 dependent package - 2.14 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.28.0
Fast Gene Set Enrichment Analysis
2 versions - Latest release: 4 months ago - 37 dependent packages - 1.09 million downloads total - 340 stars on GitHub - 1 maintainer
Top 0.5% on bioconductor.org
DESeq2 1.42.0
Differential gene expression analysis based on the negative binomial distribution
2 versions - Latest release: 4 months ago - 135 dependent packages - 2.65 million downloads total - 318 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.48.0
Analyze Illumina Infinium DNA methylation arrays
2 versions - Latest release: 4 months ago - 31 dependent packages - 774 thousand downloads total - 53 stars on GitHub - 1 maintainer
NanoMethViz 2.8.1
Visualise methlation data from Oxford Nanopore sequencing
2 versions - Latest release: 3 months ago - 4.49 thousand downloads total - 19 stars on GitHub - 1 maintainer
seqArchR 1.6.0
Identify Different Architectures of Sequence Elements
2 versions - Latest release: 4 months ago - 1 dependent package - 1.88 thousand downloads total - 1 stars on GitHub - 1 maintainer
gemma.R 2.0.0
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...
2 versions - Latest release: 4 months ago - 1.29 thousand downloads total - 7 stars on GitHub - 1 maintainer
Voyager 1.4.0
From geospatial to spatial omics
2 versions - Latest release: 3 months ago - 2.11 thousand downloads total - 57 stars on GitHub - 1 maintainer
ggkegg 1.0.13
KEGG pathway visualization by ggplot2
7 versions - Latest release: about 7 hours ago - 1.51 thousand downloads total - 183 stars on GitHub - 1 maintainer
ClassifyR 3.6.4
A framework for cross-validated classification problems, with applications to differential variab...
5 versions - Latest release: about 7 hours ago - 4 dependent packages - 19.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
proDA 1.16.0
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
2 versions - Latest release: 4 months ago - 1 dependent package - 10.1 thousand downloads total - 14 stars on GitHub - 1 maintainer
VDJdive 1.4.0
Analysis Tools for 10X V(D)J Data
2 versions - Latest release: 3 months ago - 1.03 thousand downloads total - 5 stars on GitHub - 1 maintainer
msImpute 1.12.0
Imputation of label-free mass spectrometry peptides
2 versions - Latest release: 3 months ago - 3.66 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
pRoloc 1.42.0
A unifying bioinformatics framework for spatial proteomics
2 versions - Latest release: 4 months ago - 3 dependent packages - 53.9 thousand downloads total - 14 stars on GitHub - 1 maintainer
yamss 1.28.0
Tools for high-throughput metabolomics
2 versions - Latest release: 3 months ago - 10.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
Herper 1.12.0
The Herper package is a simple toolset to install and manage conda packages and environments from R
2 versions - Latest release: 4 months ago - 6.64 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
destiny 3.16.0
Creates diffusion maps
2 versions - Latest release: 3 months ago - 4 dependent packages - 130 thousand downloads total - 67 stars on GitHub - 1 maintainer
SPOTlight 1.6.7
`SPOTlight`: Spatial Transcriptomics Deconvolution
4 versions - Latest release: 16 days ago - 5.18 thousand downloads total - 136 stars on GitHub - 1 maintainer
scRNAseqApp 1.2.2
A single-cell RNAseq Shiny app-package
3 versions - Latest release: 3 months ago - 784 downloads total - 2 stars on GitHub - 1 maintainer
gDNAx 1.0.1
Diagnostics for assessing genomic DNA contamination in RNA-seq data
2 versions - Latest release: 10 days ago - 363 downloads total - 0 stars on GitHub - 1 maintainer
crisprDesign 1.4.0
Comprehensive design of CRISPR gRNAs for nucleases and base editors
2 versions - Latest release: 3 months ago - 2 dependent packages - 2.67 thousand downloads total - 15 stars on GitHub - 1 maintainer
ideal 1.26.0
Interactive Differential Expression AnaLysis
2 versions - Latest release: 4 months ago - 13.8 thousand downloads total - 29 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.70.0
Get data from NCBI Gene Expression Omnibus (GEO)
2 versions - Latest release: 4 months ago - 47 dependent packages - 1.69 million downloads total - 80 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.0.2
LC-MS and GC-MS Data Analysis
4 versions - Latest release: about 1 month ago - 15 dependent packages - 845 thousand downloads total - 157 stars on GitHub - 1 maintainer
Top 1.1% on bioconductor.org
BiocParallel 1.36.0
Bioconductor facilities for parallel evaluation
2 versions - Latest release: 4 months ago - 356 dependent packages - 5.26 million downloads total - 62 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
qvalue 2.34.0
Q-value estimation for false discovery rate control
2 versions - Latest release: 4 months ago - 44 dependent packages - 1.47 million downloads total - 105 stars on GitHub - 2 maintainers
Top 1.9% on bioconductor.org
MSnbase 2.28.1
Base Functions and Classes for Mass Spectrometry and Proteomics
3 versions - Latest release: 4 months ago - 30 dependent packages - 380 thousand downloads total - 119 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
vsn 3.70.0
Variance stabilization and calibration for microarray data
2 versions - Latest release: 4 months ago - 29 dependent packages - 870 thousand downloads total - 1 maintainer
Top 0.2% on bioconductor.org
SummarizedExperiment 1.32.0
SummarizedExperiment container
2 versions - Latest release: 4 months ago - 590 dependent packages - 4.68 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
XVector 0.42.0
Foundation of external vector representation and manipulation in Bioconductor
2 versions - Latest release: 4 months ago - 35 dependent packages - 5.64 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
HDF5Array 1.30.1
HDF5 backend for DelayedArray objects
3 versions - Latest release: 13 days ago - 53 dependent packages - 912 thousand downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.60.0
FASTQ input and manipulation
2 versions - Latest release: 4 months ago - 36 dependent packages - 1.59 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
IRanges 2.36.0
Foundation of integer range manipulation in Bioconductor
2 versions - Latest release: 4 months ago - 545 dependent packages - 7.63 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
zlibbioc 1.48.0
An R packaged zlib-1.2.5
2 versions - Latest release: 4 months ago - 27 dependent packages - 6.01 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
S4Vectors 0.40.2
Foundation of vector-like and list-like containers in Bioconductor
4 versions - Latest release: 3 months ago - 706 dependent packages - 7.02 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.30.1
Single-Cell Analysis Toolkit for Gene Expression Data in R
3 versions - Latest release: 3 months ago - 86 dependent packages - 590 thousand downloads total - 1 maintainer
Top 0.4% on bioconductor.org
Rsamtools 2.18.0
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
2 versions - Latest release: 4 months ago - 208 dependent packages - 3.73 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
RBGL 1.78.0
An interface to the BOOST graph library
2 versions - Latest release: 4 months ago - 33 dependent packages - 1.43 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
clusterProfiler 4.10.0
A universal enrichment tool for interpreting omics data
2 versions - Latest release: 4 months ago - 53 dependent packages - 1.31 million downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.58.1
Linear Models for Microarray Data
3 versions - Latest release: 4 months ago - 315 dependent packages - 4.91 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
GenomicAlignments 1.38.2
Representation and manipulation of short genomic alignments
4 versions - Latest release: about 1 month ago - 128 dependent packages - 3.39 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
GenomeInfoDb 1.38.6
Utilities for manipulating chromosome names, including modifying them to follow a particular nami...
7 versions - Latest release: 16 days ago - 327 dependent packages - 6.73 million downloads total - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 3.28.2
Disease Ontology Semantic and Enrichment analysis
4 versions - Latest release: 3 months ago - 25 dependent packages - 1.17 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
GenomicFeatures 1.54.3
Conveniently import and query gene models
4 versions - Latest release: 28 days ago - 175 dependent packages - 3.18 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
MatrixGenerics 1.14.0
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
2 versions - Latest release: 4 months ago - 39 dependent packages - 2.71 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.70.2
Efficient manipulation of biological strings
4 versions - Latest release: 28 days ago - 324 dependent packages - 5.93 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
enrichplot 1.22.0
Visualization of Functional Enrichment Result
2 versions - Latest release: 4 months ago - 15 dependent packages - 1.1 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
DelayedArray 0.28.0
A unified framework for working transparently with on-disk and in-memory array-like datasets
2 versions - Latest release: 4 months ago - 107 dependent packages - 4.68 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
ggtree 3.10.1
an R package for visualization of tree and annotation data
3 versions - Latest release: about 15 hours ago - 25 dependent packages - 1.05 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
Biobase 2.62.0
Biobase: Base functions for Bioconductor
2 versions - Latest release: 4 months ago - 509 dependent packages - 7.55 million downloads total - 1 maintainer
Top 0.8% on bioconductor.org
BSgenome 1.70.2
Software infrastructure for efficient representation of full genomes and their SNPs
4 versions - Latest release: 16 days ago - 125 dependent packages - 1.9 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.0.16
Empirical Analysis of Digital Gene Expression Data in R
13 versions - Latest release: 8 days ago - 171 dependent packages - 2.91 million downloads total - 4 maintainers
Top 0.1% on bioconductor.org
GenomicRanges 1.54.1
Representation and manipulation of genomic intervals
3 versions - Latest release: 4 months ago - 577 dependent packages - 6 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.50.0
Surrogate Variable Analysis
2 versions - Latest release: 4 months ago - 41 dependent packages - 774 thousand downloads total - 3 maintainers
Top 1.2% on bioconductor.org
multtest 2.58.0
Resampling-based multiple hypothesis testing
2 versions - Latest release: 4 months ago - 36 dependent packages - 1.96 million downloads total - 1 maintainer
Top 0.4% on bioconductor.org
rtracklayer 1.62.0
R interface to genome annotation files and the UCSC genome browser
2 versions - Latest release: 4 months ago - 239 dependent packages - 3.71 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
SingleCellExperiment 1.24.0
S4 Classes for Single Cell Data
2 versions - Latest release: 4 months ago - 186 dependent packages - 982 thousand downloads total - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.46.0
Provides plotting capabilities for R graph objects
2 versions - Latest release: 4 months ago - 60 dependent packages - 1.47 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
VariantAnnotation 1.48.1
Annotation of Genetic Variants
3 versions - Latest release: 4 months ago - 89 dependent packages - 1.49 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
KEGGREST 1.42.0
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
2 versions - Latest release: 4 months ago - 34 dependent packages - 2.18 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.64.0
Gene set enrichment data structures and methods
2 versions - Latest release: 4 months ago - 49 dependent packages - 941 thousand downloads total - 1 maintainer
Top 0.7% on bioconductor.org
graph 1.80.0
graph: A package to handle graph data structures
2 versions - Latest release: 4 months ago - 100 dependent packages - 2.45 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
impute 1.76.0
impute: Imputation for microarray data
2 versions - Latest release: 4 months ago - 44 dependent packages - 1.42 million downloads total - 1 maintainer
Top 0.8% on bioconductor.org
flowCore 2.14.1
flowCore: Basic structures for flow cytometry data
3 versions - Latest release: about 1 month ago - 49 dependent packages - 4.75 million downloads total - 1 maintainer
Top 0.7% on bioconductor.org
genefilter 1.84.0
genefilter: methods for filtering genes from high-throughput experiments
2 versions - Latest release: 4 months ago - 65 dependent packages - 3.24 million downloads total - 1 maintainer
metabinR 1.4.0
Abundance and Compositional Based Binning of Metagenomes
2 versions - Latest release: 4 months ago - 1.04 thousand downloads total - 0 stars on GitHub - 1 maintainer
miloR 1.10.0
Differential neighbourhood abundance testing on a graph
2 versions - Latest release: 4 months ago - 9.09 thousand downloads total - 286 stars on GitHub - 1 maintainer
Top 5.6% on bioconductor.org
sesame 1.20.0
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
2 versions - Latest release: 3 months ago - 3 dependent packages - 47.2 thousand downloads total - 44 stars on GitHub - 1 maintainer
mistyR 1.10.0
Multiview Intercellular SpaTial modeling framework
3 versions - Latest release: 4 months ago - 3.46 thousand downloads total - 34 stars on GitHub - 1 maintainer
ORFik 1.22.2
Open Reading Frames in Genomics
4 versions - Latest release: 8 days ago - 2 dependent packages - 14.8 thousand downloads total - 31 stars on GitHub - 1 maintainer
martini 1.22.0
GWAS Incorporating Networks
2 versions - Latest release: 3 months ago - 6.89 thousand downloads total - 4 stars on GitHub - 1 maintainer
cogena 1.36.0
co-expressed gene-set enrichment analysis
2 versions - Latest release: 3 months ago - 17 thousand downloads total - 12 stars on GitHub - 1 maintainer
DEWSeq 1.16.2
Differential Expressed Windows Based on Negative Binomial Distribution
2 versions - Latest release: 3 months ago - 4.71 thousand downloads total - 3 stars on GitHub - 1 maintainer
RIVER 1.26.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)
2 versions - Latest release: 3 months ago - 7.94 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
mia 1.10.0
Microbiome analysis
2 versions - Latest release: 4 months ago - 5 dependent packages - 42 thousand downloads total - 43 stars on GitHub - 1 maintainer
cmapR 1.14.0
CMap Tools in R
2 versions - Latest release: 3 months ago - 19 thousand downloads total - 75 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
AnnotationDbi 1.64.1
Manipulation of SQLite-based annotations in Bioconductor
2 versions - Latest release: 3 months ago - 247 dependent packages - 5.79 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.80.0
Methods for Affymetrix Oligonucleotide Arrays
2 versions - Latest release: 3 months ago - 74 dependent packages - 1.82 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
BiocGenerics 0.48.1
S4 generic functions used in Bioconductor
2 versions - Latest release: 3 months ago - 701 dependent packages - 7.74 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.80.0
Annotation for microarrays
2 versions - Latest release: 3 months ago - 48 dependent packages - 3.5 million downloads total - 1 maintainer
SpatialFeatureExperiment 1.4.0
Integrating SpatialExperiment with Simple Features in sf
2 versions - Latest release: 3 months ago - 1 dependent package - 3.09 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
scDblFinder 1.16.0
scDblFinder
2 versions - Latest release: 4 months ago - 1 dependent package - 50.5 thousand downloads total - 123 stars on GitHub - 1 maintainer
getDEE2 1.12.0
Programmatic access to the DEE2 RNA expression dataset
2 versions - Latest release: 3 months ago - 3.32 thousand downloads total - 4 stars on GitHub - 1 maintainer
demuxmix 1.4.0
Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models
2 versions - Latest release: 3 months ago - 1 dependent package - 3.26 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
ProtGenerics 1.34.0
Generic infrastructure for Bioconductor mass spectrometry packages
2 versions - Latest release: 4 months ago - 19 dependent packages - 916 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 9.3% on bioconductor.org
BiocSingular 1.18.0
Singular Value Decomposition for Bioconductor Packages
2 versions - Latest release: 3 months ago - 27 dependent packages - 644 thousand downloads total - 6 stars on GitHub - 1 maintainer
nucleoSim 1.30.0
Generate synthetic nucleosome maps
2 versions - Latest release: 4 months ago - 1 dependent package - 9.69 thousand downloads total - 2 stars on GitHub - 1 maintainer
rTRM 1.40.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks
2 versions - Latest release: 3 months ago - 1 dependent package - 18.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
cellbaseR 1.26.0
Querying annotation data from the high performance Cellbase web
3 versions - Latest release: 3 months ago - 9.7 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: 5 months ago - 1.85 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
EnrichmentBrowser 2.32.0
Seamless navigation through combined results of set-based and network-based enrichment analysis
2 versions - Latest release: 4 months ago - 4 dependent packages - 47.8 thousand downloads total - 19 stars on GitHub - 1 maintainer
BgeeCall 1.18.1
Automatic RNA-Seq present/absent gene expression calls generation
3 versions - Latest release: 4 months ago - 4.46 thousand downloads total - 3 stars on GitHub - 1 maintainer
peakPantheR 1.16.1
Peak Picking and Annotation of High Resolution Experiments
3 versions - Latest release: 1 day ago - 4.87 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.46.1
R Interface to HDF5
3 versions - Latest release: 3 months ago - 63 dependent packages - 1.98 million downloads total - 57 stars on GitHub - 1 maintainer
scPCA 1.16.0
Sparse Contrastive Principal Component Analysis
2 versions - Latest release: 3 months ago - 6.01 thousand downloads total - 9 stars on GitHub - 1 maintainer
dreamlet 1.0.0
Cohort-scale differential expression analysis of single cell data using linear (mixed) models
1 version - Latest release: 4 months ago - 395 downloads total - 9 stars on GitHub - 1 maintainer
InterCellar 2.8.0
InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication i...
2 versions - Latest release: 3 months ago - 3.45 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 9.7% on bioconductor.org
muscat 1.16.0
Multi-sample multi-group scRNA-seq data analysis tools
2 versions - Latest release: 3 months ago - 1 dependent package - 17.5 thousand downloads total - 147 stars on GitHub - 1 maintainer