Ecosyste.ms: Packages

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

bioconductor.org packages

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Top 7.0% on bioconductor.org
a4 1.50.1
Automated Affymetrix Array Analysis Umbrella Package
3 versions - Latest release: 3 months ago - 38.3 thousand downloads total - 1 maintainer
a4Base 1.50.0
Automated Affymetrix Array Analysis Base Package
2 versions - Latest release: 6 months ago - 2 dependent packages - 38.9 thousand downloads total - 1 maintainer
a4Classif 1.50.0
Automated Affymetrix Array Analysis Classification Package
2 versions - Latest release: 6 months ago - 1 dependent package - 36.8 thousand downloads total - 1 maintainer
a4Core 1.50.0
Automated Affymetrix Array Analysis Core Package
2 versions - Latest release: 6 months ago - 3 dependent packages - 40.8 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
a4Preproc 1.50.0
Automated Affymetrix Array Analysis Preprocessing Package
2 versions - Latest release: 6 months ago - 4 dependent packages - 41 thousand downloads total - 1 maintainer
a4Reporting 1.50.0
Automated Affymetrix Array Analysis Reporting Package
2 versions - Latest release: 6 months ago - 1 dependent package - 33.7 thousand downloads total - 1 maintainer
ABarray 1.70.0
Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1...
2 versions - Latest release: 6 months ago - 42.5 thousand downloads total - 1 maintainer
abseqR 1.20.0
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
2 versions - Latest release: 6 months ago - 6.76 thousand downloads total - 0 stars on GitHub - 1 maintainer
ABSSeq 1.56.0
ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
2 versions - Latest release: 6 months ago - 22.3 thousand downloads total - 1 maintainer
acde 1.32.0
Artificial Components Detection of Differentially Expressed Genes
2 versions - Latest release: 6 months ago - 14.1 thousand downloads total - 1 maintainer
ACE 1.22.0
Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
3 versions - Latest release: 7 days ago - 8.72 thousand downloads total - 11 stars on GitHub - 1 maintainer
aCGH 1.80.0
Classes and functions for Array Comparative Genomic Hybridization data
2 versions - Latest release: 6 months ago - 5 dependent packages - 61.9 thousand downloads total - 1 maintainer
Top 5.1% on bioconductor.org
ACME 2.60.0
Algorithms for Calculating Microarray Enrichment (ACME)
3 versions - Latest release: 2 days ago - 1 dependent package - 41.6 thousand downloads total - 1 maintainer
ADaCGH2 2.42.0
Analysis of big data from aCGH experiments using parallel computing and ff objects
2 versions - Latest release: 6 months ago - 29.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
ADAM 1.18.0
ADAM: Activity and Diversity Analysis Module
2 versions - Latest release: 6 months ago - 1 dependent package - 7.04 thousand downloads total - 1 maintainer
ADAMgui 1.18.0
Activity and Diversity Analysis Module Graphical User Interface
2 versions - Latest release: 6 months ago - 6.41 thousand downloads total - 1 maintainer
adductomicsR 1.18.0
Processing of adductomic mass spectral datasets
2 versions - Latest release: 6 months ago - 6.32 thousand downloads total - 1 stars on GitHub - 1 maintainer
ADImpute 1.12.0
Adaptive Dropout Imputer (ADImpute)
2 versions - Latest release: 6 months ago - 4.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
adSplit 1.72.0
Annotation-Driven Clustering
2 versions - Latest release: 6 months ago - 36.3 thousand downloads total - 1 maintainer
adverSCarial 1.0.0
adverSCarial, generate and analyze the vulnerability of scRNA-seq classifiers to adversarial attacks
1 version - Latest release: 7 months ago - 634 downloads total - 1 maintainer
AffiXcan 1.20.0
A Functional Approach To Impute Genetically Regulated Expression
2 versions - Latest release: 6 months ago - 6.69 thousand downloads total - 1 maintainer
affxparser 1.76.0
Affymetrix File Parsing SDK
3 versions - Latest release: 9 days ago - 10 dependent packages - 323 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.82.0
Methods for Affymetrix Oligonucleotide Arrays
3 versions - Latest release: 9 days ago - 74 dependent packages - 1.85 million downloads total - 1 maintainer
Top 4.3% on bioconductor.org
affycomp 1.80.0
Graphics Toolbox for Assessment of Affymetrix Expression Measures
3 versions - Latest release: 2 days ago - 58.2 thousand downloads total - 1 maintainer
affyContam 1.60.0
structured corruption of affymetrix cel file data
2 versions - Latest release: 6 months ago - 1 dependent package - 36.3 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
affycoretools 1.76.0
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
3 versions - Latest release: 2 days ago - 2 dependent packages - 119 thousand downloads total - 1 maintainer
affyILM 1.54.0
Linear Model of background subtraction and the Langmuir isotherm
2 versions - Latest release: 6 months ago - 29.4 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
affyio 1.72.0
Tools for parsing Affymetrix data files
2 versions - Latest release: 7 months ago - 12 dependent packages - 1.52 million downloads total - 3 stars on GitHub - 1 maintainer
Top 4.8% on bioconductor.org
affylmGUI 1.78.0
GUI for limma Package with Affymetrix Microarrays
3 versions - Latest release: 2 days ago - 66 thousand downloads total - 1 maintainer
affyPLM 1.78.0
Methods for fitting probe-level models
2 versions - Latest release: 6 months ago - 9 dependent packages - 568 thousand downloads total - 0 stars on GitHub - 1 maintainer
AffyRNADegradation 1.48.0
Analyze and correct probe positional bias in microarray data due to RNA degradation
2 versions - Latest release: 6 months ago - 25.6 thousand downloads total - 1 maintainer
AGDEX 1.50.0
Agreement of Differential Expression Analysis
2 versions - Latest release: 6 months ago - 26.3 thousand downloads total - 1 maintainer
aggregateBioVar 1.12.0
Differential Gene Expression Analysis for Multi-subject scRNA-seq
2 versions - Latest release: 6 months ago - 4.58 thousand downloads total - 5 stars on GitHub - 1 maintainer
agilp 3.34.0
Agilent expression array processing package
2 versions - Latest release: 6 months ago - 36.4 thousand downloads total - 1 maintainer
Top 7.8% on bioconductor.org
AgiMicroRna 2.52.0
Processing and Differential Expression Analysis of Agilent microRNA chips
2 versions - Latest release: 6 months ago - 46.4 thousand downloads total - 1 maintainer
AHMassBank 1.2.1
MassBank Annotation Resources for AnnotationHub
3 versions - Latest release: 4 months ago - 1 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 9.3% on bioconductor.org
AIMS 1.34.0
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
2 versions - Latest release: 6 months ago - 1 dependent package - 45 thousand downloads total - 1 maintainer
airpart 1.10.0
Differential cell-type-specific allelic imbalance
2 versions - Latest release: 6 months ago - 3.15 thousand downloads total - 2 stars on GitHub - 1 maintainer
alabaster 1.2.0
Umbrella for the Alabaster Framework
2 versions - Latest release: 6 months ago - 947 downloads total - 1 maintainer
alabaster.base 1.2.1
Save Bioconductor Objects To File
2 versions - Latest release: 6 months ago - 11 dependent packages - 4.21 thousand downloads total - 1 maintainer
alabaster.bumpy 1.2.0
Save and Load BumpyMatrices to/from file
2 versions - Latest release: 6 months ago - 1 dependent package - 1.47 thousand downloads total - 1 maintainer
alabaster.files 1.0.0
Wrappers to Save Common File Formats
1 version - Latest release: 7 months ago - 695 downloads total - 1 maintainer
alabaster.mae 1.2.0
Load and Save MultiAssayExperiments
2 versions - Latest release: 6 months ago - 1 dependent package - 1.51 thousand downloads total - 1 maintainer
alabaster.matrix 1.2.0
Load and Save Artifacts from File
2 versions - Latest release: 6 months ago - 2 dependent packages - 3.49 thousand downloads total - 1 maintainer
alabaster.ranges 1.2.0
Load and Save Ranges-related Artifacts from File
2 versions - Latest release: 6 months ago - 2 dependent packages - 3.25 thousand downloads total - 1 maintainer
alabaster.sce 1.2.0
Load and Save SingleCellExperiment from File
2 versions - Latest release: 6 months ago - 2 dependent packages - 1.95 thousand downloads total - 1 maintainer
alabaster.schemas 1.2.0
Schemas for the Alabaster Framework
2 versions - Latest release: 6 months ago - 1 dependent package - 3.94 thousand downloads total - 1 maintainer
alabaster.se 1.2.0
Load and Save SummarizedExperiments from File
2 versions - Latest release: 6 months ago - 4 dependent packages - 3.33 thousand downloads total - 1 maintainer
alabaster.spatial 1.2.0
Save and Load Spatial 'Omics Data to/from File
2 versions - Latest release: 6 months ago - 1 dependent package - 1.47 thousand downloads total - 1 maintainer
alabaster.string 1.2.0
Save and Load Biostrings to/from File
2 versions - Latest release: 6 months ago - 2 dependent packages - 1.6 thousand downloads total - 1 maintainer
alabaster.vcf 1.2.0
Save and Load Variant Data to/from File
2 versions - Latest release: 6 months ago - 1 dependent package - 1.44 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
ALDEx2 1.36.0
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
3 versions - Latest release: 3 days ago - 3 dependent packages - 75.9 thousand downloads total - 24 stars on GitHub - 1 maintainer
alevinQC 1.18.1
Generate QC Reports For Alevin Output
3 versions - Latest release: 12 days ago - 7.79 thousand downloads total - 29 stars on GitHub - 1 maintainer
AllelicImbalance 1.40.0
Investigates Allele Specific Expression
2 versions - Latest release: 6 months ago - 24.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
AlphaBeta 1.16.0
Computational inference of epimutation rates and spectra from high-throughput DNA methylation dat...
2 versions - Latest release: 6 months ago - 6.96 thousand downloads total - 1 maintainer
AlphaMissenseR 1.0.0
Accessing AlphaMissense Data Resources in R
1 version - Latest release: 10 days ago - 269 downloads total - 5 stars on GitHub - 1 maintainer
alpine 1.26.0 removed
alpine
1 version - Latest release: 7 months ago - 12.2 thousand downloads total - 1 maintainer
AlpsNMR 4.6.0
Automated spectraL Processing System for NMR
3 versions - Latest release: 5 days ago - 4.79 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 8.9% on bioconductor.org
altcdfenvs 2.64.0
alternative CDF environments (aka probeset mappings)
2 versions - Latest release: 6 months ago - 1 dependent package - 38.9 thousand downloads total - 1 maintainer
AMARETTO 1.18.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...
2 versions - Latest release: 6 months ago - 7.05 thousand downloads total - 1 maintainer
AMOUNTAIN 1.28.0
Active modules for multilayer weighted gene co-expression networks: a continuous optimization app...
2 versions - Latest release: 6 months ago - 1 dependent package - 13 thousand downloads total - 1 maintainer
amplican 1.24.0
Automated analysis of CRISPR experiments
2 versions - Latest release: 6 months ago - 11.8 thousand downloads total - 9 stars on GitHub - 1 maintainer
Anaquin 2.26.0
Statistical analysis of sequins
2 versions - Latest release: 6 months ago - 11.1 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
ANCOMBC 2.6.0
Microbiome differential abudance and correlation analyses with bias correction
3 versions - Latest release: 6 days ago - 2 dependent packages - 50.4 thousand downloads total - 89 stars on GitHub - 1 maintainer
AneuFinder 1.30.0
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
2 versions - Latest release: 6 months ago - 17 thousand downloads total - 15 stars on GitHub - 1 maintainer
ANF 1.24.1
Affinity Network Fusion for Complex Patient Clustering
3 versions - Latest release: 3 months ago - 8.17 thousand downloads total - 1 maintainer
animalcules 1.18.3
Interactive microbiome analysis toolkit
4 versions - Latest release: 3 months ago - 8.28 thousand downloads total - 51 stars on GitHub - 1 maintainer
Top 6.4% on bioconductor.org
annaffy 1.74.0
Annotation tools for Affymetrix biological metadata
2 versions - Latest release: 7 months ago - 2 dependent packages - 375 thousand downloads total - 1 maintainer
annmap 1.44.0
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
2 versions - Latest release: 6 months ago - 18.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.82.0
Annotation for microarrays
3 versions - Latest release: 9 days ago - 48 dependent packages - 3.59 million downloads total - 1 maintainer
Top 0.3% on bioconductor.org
AnnotationDbi 1.66.0
Manipulation of SQLite-based annotations in Bioconductor
3 versions - Latest release: 9 days ago - 247 dependent packages - 6 million downloads total - 1 maintainer
Top 8.6% on bioconductor.org
AnnotationFilter 1.28.0
Facilities for Filtering Bioconductor Annotation Resources
3 versions - Latest release: 10 days ago - 19 dependent packages - 815 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
AnnotationForge 1.44.0
Tools for building SQLite-based annotation data packages
2 versions - Latest release: 6 months ago - 5 dependent packages - 479 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
AnnotationHub 3.10.1
Client to access AnnotationHub resources
3 versions - Latest release: 16 days ago - 87 dependent packages - 966 thousand downloads total - 13 stars on GitHub - 1 maintainer
AnnotationHubData 1.32.1
Transform public data resources into Bioconductor Data Structures
3 versions - Latest release: 3 months ago - 4 dependent packages - 34.5 thousand downloads total - 1 maintainer
Top 7.3% on bioconductor.org
annotationTools 1.76.0
Annotate microarrays and perform cross-species gene expression analyses using flat file databases
2 versions - Latest release: 6 months ago - 1 dependent package - 46.1 thousand downloads total - 1 maintainer
Top 6.8% on bioconductor.org
annotatr 1.28.0
Annotation of Genomic Regions to Genomic Annotations
2 versions - Latest release: 6 months ago - 5 dependent packages - 57.5 thousand downloads total - 25 stars on GitHub - 1 maintainer
anota 1.50.0
ANalysis Of Translational Activity (ANOTA).
2 versions - Latest release: 6 months ago - 1 dependent package - 28.8 thousand downloads total - 1 maintainer
anota2seq 1.24.0
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
2 versions - Latest release: 6 months ago - 10.5 thousand downloads total - 2 maintainers
antiProfiles 1.42.0
Implementation of gene expression anti-profiles
2 versions - Latest release: 6 months ago - 20.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
AnVIL 1.14.2
Bioconductor on the AnVIL compute environment
4 versions - Latest release: 3 months ago - 4 dependent packages - 31.2 thousand downloads total - 1 maintainer
AnVILBilling 1.12.0
Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).
2 versions - Latest release: 6 months ago - 3.26 thousand downloads total - 0 stars on GitHub - 1 maintainer
AnVILPublish 1.12.0
Publish Packages and Other Resources to AnVIL Workspaces
2 versions - Latest release: 6 months ago - 3.53 thousand downloads total - 1 maintainer
AnVILWorkflow 1.2.0
Run workflows implemented in Terra/AnVIL workspace
2 versions - Latest release: 6 months ago - 858 downloads total - 5 stars on GitHub - 1 maintainer
APAlyzer 1.16.0
A toolkit for APA analysis using RNA-seq data
2 versions - Latest release: 6 months ago - 6.54 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 8.4% on bioconductor.org
apComplex 2.68.0
Estimate protein complex membership using AP-MS protein data
2 versions - Latest release: 6 months ago - 40.6 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
apeglm 1.26.0
Approximate posterior estimation for GLM coefficients
3 versions - Latest release: 2 days ago - 10 dependent packages - 252 thousand downloads total - 1 maintainer
APL 1.8.0
Association Plots
4 versions - Latest release: 9 days ago - 2.83 thousand downloads total - 15 stars on GitHub - 1 maintainer
appreci8R 1.20.2
appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity an...
3 versions - Latest release: 3 months ago - 7.13 thousand downloads total - 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: 1 day ago - 3 dependent packages - 324 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
ArrayExpress 1.64.0
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures:...
3 versions - Latest release: 1 day ago - 1 dependent package - 131 thousand downloads total - 1 maintainer
ArrayExpressHTS 1.50.0 removed
ArrayExpress High Throughput Sequencing Processing Pipeline
1 version - Latest release: 7 months ago - 17.8 thousand downloads total - 2 maintainers
arrayMvout 1.60.0
multivariate outlier detection for expression array QA
2 versions - Latest release: 6 months ago - 33 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
arrayQuality 1.80.0
Assessing array quality on spotted arrays
2 versions - Latest release: 6 months ago - 60.1 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
arrayQualityMetrics 3.60.0
Quality metrics report for microarray data sets
3 versions - Latest release: 3 days ago - 181 thousand downloads total - 1 stars on GitHub - 1 maintainer
ARRmNormalization 1.42.0
Adaptive Robust Regression normalization for Illumina methylation data
2 versions - Latest release: 6 months ago - 20.9 thousand downloads total - 1 maintainer
artMS 1.20.0
Analytical R tools for Mass Spectrometry
2 versions - Latest release: 6 months ago - 8.75 thousand downloads total - 1 maintainer
ASAFE 1.28.0
Ancestry Specific Allele Frequency Estimation
2 versions - Latest release: 6 months ago - 9.78 thousand downloads total - 1 maintainer
ASEB 1.46.3
Predict Acetylated Lysine Sites
2 versions - Latest release: 6 months ago - 23.9 thousand downloads total - 1 maintainer
ASGSCA 1.36.0
Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation M...
2 versions - Latest release: 6 months ago - 16.8 thousand downloads total - 1 maintainer