Ecosyste.ms: Packages

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

bioconductor.org "QualityControl" keyword

SPIAT 1.6.0
Spatial Image Analysis of Tissues
5 versions - Latest release: about 1 month ago - 3.28 thousand downloads total - 16 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: about 1 month ago - 2 dependent packages - 50.1 thousand downloads total - 52 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.50.0
Analyze Illumina Infinium DNA methylation arrays
3 versions - Latest release: about 1 month ago - 31 dependent packages - 789 thousand downloads total - 58 stars on GitHub - 1 maintainer
ideal 1.28.0
Interactive Differential Expression AnaLysis
3 versions - Latest release: about 1 month ago - 14.6 thousand downloads total - 29 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.56.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
3 versions - Latest release: 28 days ago - 10 dependent packages - 336 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
Rsubread 2.18.0
Mapping, quantification and variant analysis of sequencing data
4 versions - Latest release: 28 days ago - 14 dependent packages - 313 thousand downloads total - 2 maintainers
SpotSweeper 0.99.5
Spatially-aware quality control for spatial transcriptomics
2 versions - Latest release: about 1 month ago - 137 downloads total - 0 stars on GitHub - 1 maintainer
CaMutQC 1.0.0
An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations
1 version - Latest release: about 1 month ago - 373 downloads total - 6 stars on GitHub - 1 maintainer
tidyomics 0.99.7
Easily install and load the tidyomics ecosystem
2 versions - Latest release: about 1 month ago - 366 downloads total - 18 stars on GitHub - 1 maintainer
mobileRNA 1.0.0
mobileRNA: Investigate the RNA mobilome & population-scale changes
2 versions - Latest release: about 1 month ago - 405 downloads total - 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: about 1 month ago - 30 dependent packages - 397 thousand downloads total - 120 stars on GitHub - 1 maintainer
proDA 1.16.0
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
3 versions - Latest release: 7 months ago - 1 dependent package - 11.6 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 0.4% on bioconductor.org
Rsamtools 2.20.0
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
3 versions - Latest release: about 1 month ago - 212 dependent packages - 3.92 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.32.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
4 versions - Latest release: about 1 month ago - 96 dependent packages - 625 thousand downloads total - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R
14 versions - Latest release: about 1 month ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
Top 1.3% on bioconductor.org
ShortRead 1.62.0
FASTQ input and manipulation
3 versions - Latest release: about 1 month ago - 36 dependent packages - 1.63 million downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.60.0
Linear Models for Microarray Data
5 versions - Latest release: about 1 month ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
tidySummarizedExperiment 1.14.0
Brings SummarizedExperiment to the Tidyverse
3 versions - Latest release: 21 days ago - 5 dependent packages - 10.5 thousand downloads total - 19 stars on GitHub - 1 maintainer
dreamlet 1.2.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...
3 versions - Latest release: 28 days ago - 1.3 thousand downloads total - 9 stars on GitHub - 1 maintainer
GloScope 1.0.0
Population-level Representation on scRNA-Seq data
2 versions - Latest release: 7 months ago - 924 downloads total - 1 stars on GitHub - 1 maintainer
hermes 1.6.1 💰
Preprocessing, analyzing, and reporting of RNA-seq data
4 versions - Latest release: about 2 months ago - 3.31 thousand downloads total - 11 stars on GitHub - 1 maintainer
ChromSCape 1.12.0
Analysis of single-cell epigenomics datasets with a Shiny App
3 versions - Latest release: 7 months ago - 4.34 thousand downloads total - 14 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis
2 versions - Latest release: 7 months ago - 881 downloads total - 0 stars on GitHub - 1 maintainer
CytoPipeline 1.4.0
Automation and visualization of flow cytometry data analysis pipelines
3 versions - Latest release: 24 days ago - 2 dependent packages - 1.97 thousand downloads total - 3 stars on GitHub - 1 maintainer
BioQC 1.30.0
Detect tissue heterogeneity in expression profiles with gene sets
3 versions - Latest release: 6 months ago - 17.4 thousand downloads total - 5 stars on GitHub - 1 maintainer
qPLEXanalyzer 1.20.0
Tools for quantitative proteomics data analysis
3 versions - Latest release: 6 months ago - 7.02 thousand downloads total - 1 stars on GitHub - 1 maintainer
erccdashboard 1.36.0
Assess Differential Gene Expression Experiments with ERCC Controls
3 versions - Latest release: 6 months ago - 19 thousand downloads total - 7 stars on GitHub - 1 maintainer
shinyMethyl 1.38.0
Interactive visualization for Illumina methylation arrays
3 versions - Latest release: 6 months ago - 24.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
interactiveDisplayBase 1.40.0
Base package for enabling powerful shiny web displays of Bioconductor objects
3 versions - Latest release: 7 months ago - 3 dependent packages - 802 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
Rqc 1.36.0
Quality Control Tool for High-Throughput Sequencing Data
3 versions - Latest release: 6 months ago - 31.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
lipidr 2.16.0
Data Mining and Analysis of Lipidomics Datasets
3 versions - Latest release: 6 months ago - 1 dependent package - 10.2 thousand downloads total - 25 stars on GitHub - 1 maintainer
CytoPipelineGUI 1.0.0
GUI's for visualization of flow cytometry data analysis pipelines
2 versions - Latest release: 7 months ago - 921 downloads total - 0 stars on GitHub - 1 maintainer
scmeth 1.22.0
Functions to conduct quality control analysis in methylation data
3 versions - Latest release: 6 months ago - 1 dependent package - 8.27 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
scuttle 1.12.0
Single-Cell RNA-Seq Analysis Utilities
3 versions - Latest release: 7 months ago - 41 dependent packages - 548 thousand downloads total - 1 maintainer
EpiCompare 1.6.7
Comparison, Benchmarking & QC of Epigenomic Datasets
9 versions - Latest release: about 2 months ago - 2.13 thousand downloads total - 12 stars on GitHub - 1 maintainer
affyPLM 1.78.0
Methods for fitting probe-level models
3 versions - Latest release: 7 months ago - 9 dependent packages - 569 thousand downloads total - 0 stars on GitHub - 1 maintainer
REMP 1.26.0
Repetitive Element Methylation Prediction
3 versions - Latest release: 6 months ago - 11.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
cummeRbund 2.44.0
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
3 versions - Latest release: 7 months ago - 576 thousand downloads total - 1 maintainer
scruff 1.20.0
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
3 versions - Latest release: 6 months ago - 7.81 thousand downloads total - 8 stars on GitHub - 1 maintainer
DegNorm 1.12.0
DegNorm: degradation normalization for RNA-seq data
3 versions - Latest release: 6 months ago - 4.38 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 8.7% on bioconductor.org
regionReport 1.36.0
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
3 versions - Latest release: 6 months ago - 1 dependent package - 24.6 thousand downloads total - 9 stars on GitHub - 1 maintainer
PeacoQC 1.12.0
Peak-based selection of high quality cytometry data
3 versions - Latest release: 6 months ago - 1 dependent package - 7.69 thousand downloads total - 14 stars on GitHub - 1 maintainer
MAGAR 1.10.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...
3 versions - Latest release: 7 months ago - 4.57 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
isobar 1.48.0
Analysis and quantitation of isobarically tagged MSMS proteomics data
3 versions - Latest release: 6 months ago - 35.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
MBECS 1.6.0
Evaluation and correction of batch effects in microbiome data-sets
3 versions - Latest release: 6 months ago - 2.63 thousand downloads total - 4 stars on GitHub - 1 maintainer
scifer 1.4.0
Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences
3 versions - Latest release: 7 months ago - 1.72 thousand downloads total - 5 stars on GitHub - 1 maintainer
standR 1.6.0
Spatial transcriptome analyses of Nanostring's DSP data in R
3 versions - Latest release: 6 months ago - 3.38 thousand downloads total - 15 stars on GitHub - 1 maintainer
RNAinteract 1.50.0
Estimate Pairwise Interactions from multidimensional features
3 versions - Latest release: 7 months ago - 23.7 thousand downloads total - 1 maintainer
UMI4Cats 1.12.0
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
3 versions - Latest release: 7 months ago - 3.93 thousand downloads total - 4 stars on GitHub - 1 maintainer
MsQuality 1.2.1
MsQuality - Quality metric calculation from Spectra and MsExperiment objects
4 versions - Latest release: 2 months ago - 1.6 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 9.5% on bioconductor.org
nucleR 2.34.0
Nucleosome positioning package for R
3 versions - Latest release: 7 months ago - 27.2 thousand downloads total - 1 maintainer
GBScleanR 1.8.0
Error correction tool for noisy genotyping by sequencing (GBS) data
3 versions - Latest release: about 1 month ago - 2.17 thousand downloads total - 0 stars on GitHub - 1 maintainer
contiBAIT 1.30.0
Improves Early Build Genome Assemblies using Strand-Seq Data
3 versions - Latest release: 7 months ago - 10.7 thousand downloads total - 1 maintainer
Basic4Cseq 1.38.0
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
3 versions - Latest release: 7 months ago - 20.6 thousand downloads total - 1 maintainer
RiboDiPA 1.10.0
Differential pattern analysis for Ribo-seq data
3 versions - Latest release: 7 months ago - 3.28 thousand downloads total - 1 maintainer
Top 5.6% on bioconductor.org
sesame 1.22.0
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
3 versions - Latest release: 23 days ago - 4 dependent packages - 50.3 thousand downloads total - 48 stars on GitHub - 1 maintainer
abseqR 1.20.0
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
3 versions - Latest release: 7 months ago - 7.28 thousand downloads total - 0 stars on GitHub - 1 maintainer
SNAGEE 1.42.0
Signal-to-Noise applied to Gene Expression Experiments
3 versions - Latest release: 7 months ago - 18.3 thousand downloads total - 1 maintainer
artMS 1.20.0
Analytical R tools for Mass Spectrometry
3 versions - Latest release: 7 months ago - 9.23 thousand downloads total - 1 maintainer
Top 6.6% on bioconductor.org
methylumi 2.48.0
Handle Illumina methylation data
3 versions - Latest release: 7 months ago - 7 dependent packages - 296 thousand downloads total - 8 stars on GitHub - 1 maintainer
OSAT 1.50.0
OSAT: Optimal Sample Assignment Tool
3 versions - Latest release: 7 months ago - 21.7 thousand downloads total - 1 maintainer
shinyepico 1.10.0
ShinyÉPICo
3 versions - Latest release: 7 months ago - 3.54 thousand downloads total - 3 stars on GitHub - 1 maintainer
Guitar 2.18.0
Guitar
3 versions - Latest release: 7 months ago - 18.4 thousand downloads total - 1 maintainer
MethylAid 1.36.0
Visual and interactive quality control of large Illumina DNA Methylation array data sets
3 versions - Latest release: 7 months ago - 18.5 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
altcdfenvs 2.64.0
alternative CDF environments (aka probeset mappings)
3 versions - Latest release: 7 months ago - 1 dependent package - 39.6 thousand downloads total - 1 maintainer
doppelgangR 1.30.0
Identify likely duplicate samples from genomic or meta-data
3 versions - Latest release: 7 months ago - 12.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
TargetDecoy 1.8.0
Diagnostic Plots to Evaluate the Target Decoy Approach
3 versions - Latest release: 7 months ago - 2.39 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
OLIN 1.80.0
Optimized local intensity-dependent normalisation of two-color microarrays
3 versions - Latest release: 7 months ago - 2 dependent packages - 31 thousand downloads total - 1 maintainer
CuratedAtlasQueryR 1.2.0
Queries the Human Cell Atlas
3 versions - Latest release: 27 days ago - 1.07 thousand downloads total - 77 stars on GitHub - 1 maintainer
Scale4C 1.24.0
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
3 versions - Latest release: 7 months ago - 7.48 thousand downloads total - 1 maintainer
MQmetrics 1.10.0
Quality Control of Protemics Data
3 versions - Latest release: 7 months ago - 2.66 thousand downloads total - 1 maintainer
SICtools 1.32.0
Find SNV/Indel differences between two bam files with near relationship
3 versions - Latest release: 7 months ago - 9.24 thousand downloads total - 1 maintainer
BatchQC 1.30.0
Batch Effects Quality Control Software
3 versions - Latest release: 6 months ago - 20.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
segmentSeq 2.36.0
Methods for identifying small RNA loci from high-throughput sequencing data
3 versions - Latest release: 7 months ago - 34.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
omicsPrint 1.22.0
Cross omic genetic fingerprinting
3 versions - Latest release: 7 months ago - 7.42 thousand downloads total - 1 maintainer
RITAN 1.26.0
Rapid Integration of Term Annotation and Network resources
3 versions - Latest release: 7 months ago - 9.59 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
RPA 1.58.0
RPA: Robust Probabilistic Averaging for probe-level analysis
3 versions - Latest release: 7 months ago - 1 dependent package - 30.5 thousand downloads total - 1 maintainer
qckitfastq 1.18.0
FASTQ Quality Control
3 versions - Latest release: 7 months ago - 6.42 thousand downloads total - 1 maintainer
ppcseq 1.10.0
Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models
3 versions - Latest release: 7 months ago - 2.85 thousand downloads total - 6 stars on GitHub - 1 maintainer
ffpe 1.46.0
Quality assessment and control for FFPE microarray expression data
3 versions - Latest release: 7 months ago - 25.1 thousand downloads total - 1 maintainer
conumee 1.36.0
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
3 versions - Latest release: 7 months ago - 23.8 thousand downloads total - 1 maintainer
MSstatsQCgui 1.22.0
A graphical user interface for MSstatsQC package
3 versions - Latest release: 7 months ago - 6.85 thousand downloads total - 1 maintainer
SingleMoleculeFootprinting 1.10.0
Analysis tools for Single Molecule Footprinting (SMF) data
3 versions - Latest release: 7 months ago - 2.89 thousand downloads total - 2 stars on GitHub - 1 maintainer
phenomis 1.4.0
Postprocessing and univariate analysis of omics data
3 versions - Latest release: 7 months ago - 1.98 thousand downloads total - 1 maintainer
GmicR 1.16.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...
3 versions - Latest release: 7 months ago - 5.69 thousand downloads total - 1 maintainer
IONiseR 2.26.0
Quality Assessment Tools for Oxford Nanopore MinION data
3 versions - Latest release: 7 months ago - 16 thousand downloads total - 1 maintainer
NanoTube 1.8.0
An Easy Pipeline for NanoString nCounter Data Analysis
3 versions - Latest release: 7 months ago - 3.18 thousand downloads total - 1 maintainer
MSstatsQC 2.20.0
Longitudinal system suitability monitoring and quality control for proteomic experiments
3 versions - Latest release: 7 months ago - 1 dependent package - 9.18 thousand downloads total - 1 maintainer
bigmelon 1.28.0
Illumina methylation array analysis for large experiments
3 versions - Latest release: 7 months ago - 12.3 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
ChIPQC 1.38.0
Quality metrics for ChIPseq data
3 versions - Latest release: 7 months ago - 58.3 thousand downloads total - 2 maintainers
marr 1.12.0
Maximum rank reproducibility
3 versions - Latest release: 7 months ago - 3.29 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 9.3% on bioconductor.org
MAGeCKFlute 2.6.0
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
3 versions - Latest release: 7 months ago - 1 dependent package - 32.7 thousand downloads total - 1 maintainer
basecallQC 1.26.0
Working with Illumina Basecalling and Demultiplexing input and output files
3 versions - Latest release: 7 months ago - 10.9 thousand downloads total - 1 maintainer
skewr 1.34.0
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
3 versions - Latest release: 7 months ago - 11.7 thousand downloads total - 1 maintainer
CSSP 1.40.0 removed
ChIP-Seq Statistical Power
2 versions - Latest release: 7 months ago - 17.8 thousand downloads total
Spaniel 1.16.0
Spatial Transcriptomics Analysis
3 versions - Latest release: 7 months ago - 6.46 thousand downloads total - 1 maintainer
flowCut 1.12.0
Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis
3 versions - Latest release: 7 months ago - 6.64 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
interactiveDisplay 1.40.0
Package for enabling powerful shiny web displays of Bioconductor objects
3 versions - Latest release: 7 months ago - 1 dependent package - 39.9 thousand downloads total - 1 maintainer
snm 1.50.0
Supervised Normalization of Microarrays
3 versions - Latest release: 7 months ago - 1 dependent package - 35.5 thousand downloads total - 1 maintainer
scTGIF 1.16.0
Cell type annotation for unannotated single-cell RNA-Seq data
3 versions - Latest release: 7 months ago - 1 dependent package - 6.23 thousand downloads total - 1 maintainer
Related Keywords
Software 231 Preprocessing 94 Sequencing 92 ImmunoOncology 72 GeneExpression 66 Visualization 63 Microarray 61 DataImport 61 Normalization 61 RNASeq 55 DifferentialExpression 51 Coverage 32 Clustering 32 TwoChannel 32 Proteomics 30 BatchEffect 30 MassSpectrometry 29 Alignment 27 Transcriptomics 27 DNAMethylation 26 SingleCell 25 Genetics 24 MultipleComparison 24 OneChannel 21 Transcription 21 ChIPSeq 18 GeneSetEnrichment 18 Regression 18 ReportWriting 18 Epigenetics 17 Infrastructure 17 GUI 16 DifferentialMethylation 13 FunctionalGenomics 13 bioconductor 13 MethylationArray 12 DataRepresentation 12 r 12 Classification 12 Bayesian 11 TimeCourse 11 SystemsBiology 10 Metabolomics 10 ShinyApps 10 BiomedicalInformatics 9 CopyNumberVariation 9 CellBiology 9 DimensionReduction 9 PrincipalComponent 9 GeneRegulation 8 FlowCytometry 8 WorkflowStep 8 ATACSeq 8 mRNAMicroarray 8 CpGIsland 7 AlternativeSplicing 7 DifferentialSplicing 7 ExperimentalDesign 7 Network 7 MethylSeq 7 SNP 7 GeneticVariability 6 GenomeAnnotation 6 Pathways 6 SequenceMatching 6 ProprietaryPlatforms 6 StatisticalMethod 6 GraphAndNetwork 6 proteomics 5 DNASeq 5 Annotation 5 CellBasedAssays 5 GO 5 AssayDomain 5 CRISPR 4 qPCR 4 WholeGenome 4 RiboSeq 4 ExonArray 4 shiny 4 mass-spectrometry 4 tidyverse 4 MultiChannel 4 Spatial 4 bioconductor-package 3 Lipidomics 3 MicrotitrePlateAssay 3 Bioinformatics 3 single-cell 3 HighThroughputSequencing 3 KEGG 3 MultipleComparisons 3 NucleosomePositioning 3 rstats 3 deseq2 3 edger 3 MicroRNAArray 3 SangerSeq 3 bioinformatics 3 Cheminformatics 3