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

bioconductor.org "QualityControl" keyword

Top 0.3% on bioconductor.org
limma 3.68.3
Linear Models for Microarray and Omics Data
20 versions - Latest release: about 2 hours ago - 322 dependent packages - 7.18 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.40.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
11 versions - Latest release: 19 days ago - 96 dependent packages - 1.12 million downloads total - 1 maintainer
clstutils 1.60.0
Tools for performing taxonomic assignment
7 versions - Latest release: about 8 hours ago - 32.4 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.64.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
7 versions - Latest release: 21 days ago - 10 dependent packages - 413 thousand downloads total - 1 maintainer
ibh 1.60.0
Interaction Based Homogeneity for Evaluating Gene Lists
7 versions - Latest release: about 11 hours ago - 30.8 thousand downloads total - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.10.0
Empirical Analysis of Digital Gene Expression Data in R
27 versions - Latest release: 21 days ago - 181 dependent packages - 4.42 million downloads total - 4 maintainers
DAPAR 1.44.0
Tools for the Differential Analysis of Proteins Abundance with R
12 versions - Latest release: 1 day ago - 1 dependent package - 32.6 thousand downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.70.0
FASTQ input and manipulation
8 versions - Latest release: 20 days ago - 36 dependent packages - 2.01 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.58.0
Analyze Illumina Infinium DNA methylation arrays
9 versions - Latest release: 19 days ago - 31 dependent packages - 967 thousand downloads total - 64 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
Rsubread 2.26.0
Mapping, quantification and variant analysis of sequencing data
9 versions - Latest release: 20 days ago - 14 dependent packages - 428 thousand downloads total - 2 maintainers
Top 4.7% on bioconductor.org
RnBeads 2.30.0
RnBeads
7 versions - Latest release: 2 days ago - 1 dependent package - 83.5 thousand downloads total - 1 maintainer
OSAT 1.60.0
OSAT: Optimal Sample Assignment Tool
7 versions - Latest release: 2 days ago - 31.6 thousand downloads total - 1 maintainer
PeacoQC 1.22.0
Peak-based selection of high quality cytometry data
7 versions - Latest release: 2 days ago - 1 dependent package - 22.1 thousand downloads total - 14 stars on GitHub - 1 maintainer
countsimQC 1.30.0
Compare Characteristic Features of Count Data Sets
8 versions - Latest release: 2 days ago - 1 dependent package - 28 thousand downloads total - 29 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
MSnbase 2.37.0
Base Functions and Classes for Mass Spectrometry and Proteomics
9 versions - Latest release: 19 days ago - 30 dependent packages - 610 thousand downloads total - 123 stars on GitHub - 1 maintainer
tidySummarizedExperiment 1.22.0
Brings SummarizedExperiment to the Tidyverse
8 versions - Latest release: 2 days ago - 5 dependent packages - 25.9 thousand downloads total - 30 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
interactiveDisplayBase 1.48.0 removed
Base package for enabling powerful shiny web displays of Bioconductor objects
6 versions - Latest release: 6 months ago - 3 dependent packages - 1.03 million downloads total - 1 maintainer
GloScope 2.2.0
Population-level Representation on scRNA-Seq data
7 versions - Latest release: 3 days ago - 7.39 thousand downloads total - 1 stars on GitHub - 1 maintainer
CytoMDS 1.8.0
Low Dimensions projection of cytometry samples
6 versions - Latest release: 3 days ago - 6.42 thousand downloads total - 1 stars on GitHub - 1 maintainer
DspikeIn 1.2.0
Estimating Absolute Abundance from Microbial Spike-in Controls
3 versions - Latest release: 3 days ago - 1.75 thousand downloads total - 16 stars on GitHub - 1 maintainer
dreamlet 1.10.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...
8 versions - Latest release: 3 days ago - 11.2 thousand downloads total - 20 stars on GitHub - 1 maintainer
RiboProfiling 1.42.0
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
7 versions - Latest release: 4 days ago - 27.6 thousand downloads total - 1 maintainer
chevreulPlot 1.4.0
Plots used in the chevreulPlot package
3 versions - Latest release: 4 days ago - 3.46 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.3% on bioconductor.org
dyebias 1.72.0
The GASSCO method for correcting for slide-dependent gene-specific dye bias
7 versions - Latest release: 4 days ago - 39.7 thousand downloads total - 1 maintainer
SICtools 1.42.0
Find SNV/Indel differences between two bam files with near relationship
7 versions - Latest release: 4 days ago - 19.6 thousand downloads total - 1 maintainer
notame 1.2.0
Workflow for non-targeted LC-MS metabolic profiling
3 versions - Latest release: 4 days ago - 2.28 thousand downloads total - 3 stars on GitHub - 1 maintainer
SNAGEE 1.52.0
Signal-to-Noise applied to Gene Expression Experiments
7 versions - Latest release: 4 days ago - 27.4 thousand downloads total - 1 maintainer
SCOPE 1.24.0
A normalization and copy number estimation method for single-cell DNA sequencing
7 versions - Latest release: 4 days ago - 13.2 thousand downloads total - 1 maintainer
tidybulk 2.2.0
Brings transcriptomics to the tidyverse
9 versions - Latest release: 4 days ago - 1 dependent package - 27.8 thousand downloads total - 176 stars on GitHub - 1 maintainer
MethylAid 1.46.0
Visual and interactive quality control of large Illumina DNA Methylation array data sets
7 versions - Latest release: 4 days ago - 30.8 thousand downloads total - 1 maintainer
AffyRNADegradation 1.58.0
Analyze and correct probe positional bias in microarray data due to RNA degradation
7 versions - Latest release: 5 days ago - 37.8 thousand downloads total - 1 maintainer
traseR 1.42.0
GWAS trait-associated SNP enrichment analyses in genomic intervals
7 versions - Latest release: 5 days ago - 21.3 thousand downloads total
MSstatsConvert 1.22.0
Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
10 versions - Latest release: 5 days ago - 6 dependent packages - 47.2 thousand downloads total - 1 maintainer
DiscoRhythm 1.28.0
Interactive Workflow for Discovering Rhythmicity in Biological Data
7 versions - Latest release: 5 days ago - 15.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
Rfastp 1.22.0
An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX ...
9 versions - Latest release: 5 days ago - 17.3 thousand downloads total - 1 maintainer
flowCut 1.22.0
Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis
7 versions - Latest release: 5 days ago - 16.2 thousand downloads total - 1 maintainer
scruff 1.30.0
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
8 versions - Latest release: 5 days ago - 16.5 thousand downloads total - 8 stars on GitHub - 1 maintainer
CaMutQC 1.8.0
An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations
8 versions - Latest release: 5 days ago - 6.31 thousand downloads total - 7 stars on GitHub - 1 maintainer
marr 1.22.0
Maximum rank reproducibility
7 versions - Latest release: 5 days ago - 10.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
ChIPQC 1.48.2
Quality metrics for ChIPseq data
7 versions - Latest release: 5 days ago - 79.2 thousand downloads total - 2 maintainers
CONFESS 1.40.0
Cell OrderiNg by FluorEScence Signal
7 versions - Latest release: 5 days ago - 20.3 thousand downloads total - 1 maintainer
qcmetrics 1.50.0
A Framework for Quality Control
8 versions - Latest release: 6 days ago - 1 dependent package - 30.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
pcaExplorer 3.6.0
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
7 versions - Latest release: 6 days ago - 2 dependent packages - 69.3 thousand downloads total - 56 stars on GitHub - 1 maintainer
MSstatsPTM 2.14.0
Statistical Characterization of Post-translational Modifications
13 versions - Latest release: 6 days ago - 2 dependent packages - 21.2 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 9.4% on bioconductor.org
R453Plus1Toolbox 1.62.0
A package for importing and analyzing data from Roche's Genome Sequencer System
8 versions - Latest release: 6 days ago - 36.8 thousand downloads total - 1 maintainer
Doscheda 1.34.0
A DownStream Chemo-Proteomics Analysis Pipeline
7 versions - Latest release: 6 days ago - 17.6 thousand downloads total - 1 maintainer
MSstatsQC 2.30.0
Longitudinal system suitability monitoring and quality control for proteomic experiments
7 versions - Latest release: 6 days ago - 1 dependent package - 18.3 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
nucleR 2.44.0
Nucleosome positioning package for R
7 versions - Latest release: 6 days ago - 39.3 thousand downloads total - 1 maintainer
bandle 1.16.0
An R package for the Bayesian analysis of differential subcellular localisation experiments
7 versions - Latest release: 6 days ago - 9.85 thousand downloads total - 4 stars on GitHub - 1 maintainer
scifer 1.14.0
Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences
8 versions - Latest release: 6 days ago - 8.42 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
dupRadar 1.42.0
Assessment of duplication rates in RNA-Seq datasets
7 versions - Latest release: 7 days ago - 62.5 thousand downloads total - 2 stars on GitHub - 2 maintainers
crumblr 1.4.0
Count ratio uncertainty modeling base linear regression
3 versions - Latest release: 7 days ago - 3.44 thousand downloads total - 6 stars on GitHub - 1 maintainer
massiR 1.48.0
massiR: MicroArray Sample Sex Identifier
7 versions - Latest release: 7 days ago - 26.4 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
mdqc 1.74.0
Mahalanobis Distance Quality Control for microarrays
7 versions - Latest release: 7 days ago - 1 dependent package - 45.4 thousand downloads total - 1 maintainer
snm 1.60.0
Supervised Normalization of Microarrays
7 versions - Latest release: 7 days ago - 1 dependent package - 47.7 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
MSstats 4.20.0
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experi...
13 versions - Latest release: 7 days ago - 8 dependent packages - 99.7 thousand downloads total - 1 maintainer
shinyepico 1.20.0
ShinyÉPICo
7 versions - Latest release: 7 days ago - 11.1 thousand downloads total - 5 stars on GitHub - 1 maintainer
qckitfastq 1.26.0 removed
FASTQ Quality Control
6 versions - Latest release: 6 months ago - 11.5 thousand downloads total - 1 maintainer
CRISPRball 1.8.0
Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filte...
6 versions - Latest release: 7 days ago - 5.86 thousand downloads total - 11 stars on GitHub - 1 maintainer
scBFA 1.26.0
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile...
7 versions - Latest release: 7 days ago - 13.3 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
HELP 1.70.0
Tools for HELP data analysis
7 versions - Latest release: 7 days ago - 39.5 thousand downloads total - 1 maintainer
AssessORF 1.30.0
Assess Gene Predictions Using Proteomics and Evolutionary Conservation
7 versions - Latest release: 8 days ago - 17.8 thousand downloads total - 1 maintainer
ChIPexoQual 1.36.0
ChIPexoQual
7 versions - Latest release: 8 days ago - 21.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 8.4% on bioconductor.org
TEQC 4.34.0
Quality control for target capture experiments
7 versions - Latest release: 8 days ago - 39 thousand downloads total - 1 maintainer
GBScleanR 2.6.0
Error correction tool for noisy genotyping by sequencing (GBS) data
13 versions - Latest release: 8 days ago - 9.87 thousand downloads total - 4 stars on GitHub - 1 maintainer
chevreulProcess 1.4.0
Tools for managing SingleCellExperiment objects as projects
3 versions - Latest release: 8 days ago - 3.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
GmicR 1.26.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...
7 versions - Latest release: 8 days ago - 13.1 thousand downloads total - 1 maintainer
artMS 1.29.0
Analytical R tools for Mass Spectrometry
7 versions - Latest release: 8 days ago - 18.4 thousand downloads total - 1 maintainer
ppcseq 1.20.0
Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models
7 versions - Latest release: 8 days ago - 10.1 thousand downloads total - 8 stars on GitHub - 1 maintainer
chevreulShiny 1.4.0
Tools for managing SingleCellExperiment objects as projects
4 versions - Latest release: 8 days ago - 3.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
tidySingleCellExperiment 1.22.0
Brings SingleCellExperiment to the Tidyverse
8 versions - Latest release: 8 days ago - 4 dependent packages - 23.7 thousand downloads total - 36 stars on GitHub - 1 maintainer
affyPLM 1.88.0
Methods for fitting probe-level models
7 versions - Latest release: 9 days ago - 9 dependent packages - 642 thousand downloads total - 0 stars on GitHub - 1 maintainer
ideal 2.6.0
Interactive Differential Expression AnaLysis
7 versions - Latest release: 8 days ago - 25.2 thousand downloads total - 29 stars on GitHub - 1 maintainer
Top 8.2% on bioconductor.org
Rqc 1.46.0
Quality Control Tool for High-Throughput Sequencing Data
7 versions - Latest release: 9 days ago - 50.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
GENESIS 2.42.0
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzi...
7 versions - Latest release: 9 days ago - 1 dependent package - 87.3 thousand downloads total - 40 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
scuttle 1.22.0
Legacy Utilities for Single-Cell RNA-Seq Analysis
7 versions - Latest release: 9 days ago - 41 dependent packages - 1.14 million downloads total - 1 maintainer
Top 5.4% on bioconductor.org
limmaGUI 1.88.0
GUI for limma Package With Two Color Microarrays
7 versions - Latest release: 9 days ago - 60.3 thousand downloads total - 1 maintainer
cellity 1.40.0
Quality Control for Single-Cell RNA-seq Data
7 versions - Latest release: 9 days ago - 22.3 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
beadarray 2.62.0
Quality assessment and low-level analysis for Illumina BeadArray data
9 versions - Latest release: 9 days ago - 5 dependent packages - 238 thousand downloads total - 1 maintainer
pvac 1.60.0
PCA-based gene filtering for Affymetrix arrays
7 versions - Latest release: 9 days ago - 33.3 thousand downloads total - 2 maintainers
RadioGx 2.16.0
Analysis of Large-Scale Radio-Genomic Data
7 versions - Latest release: 9 days ago - 13.7 thousand downloads total - 1 maintainer
SPIAT 1.14.0
Spatial Image Analysis of Tissues
12 versions - Latest release: 9 days ago - 12.6 thousand downloads total - 24 stars on GitHub - 1 maintainer
ggspavis 1.18.0
Visualization functions for spatial transcriptomics data
11 versions - Latest release: 9 days ago - 1 dependent package - 19.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
KnowSeq 1.25.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
7 versions - Latest release: 10 days ago - 15.4 thousand downloads total - 1 maintainer
bigmelon 1.38.0
Illumina methylation array analysis for large experiments
7 versions - Latest release: 10 days ago - 23.8 thousand downloads total - 1 maintainer
AMARETTO 1.28.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...
7 versions - Latest release: 10 days ago - 18.8 thousand downloads total - 1 maintainer
hermes 1.16.0 💰
Preprocessing, analyzing, and reporting of RNA-seq data
9 versions - Latest release: 10 days ago - 13.9 thousand downloads total - 12 stars on GitHub - 1 maintainer
lipidr 2.26.0
Data Mining and Analysis of Lipidomics Datasets
8 versions - Latest release: 10 days ago - 1 dependent package - 20.4 thousand downloads total - 31 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
arrayQualityMetrics 3.68.0
Quality metrics report for microarray data sets
8 versions - Latest release: 10 days ago - 218 thousand downloads total - 1 stars on GitHub - 1 maintainer
alevinQC 1.28.0
Generate QC Reports For Alevin Output
8 versions - Latest release: 10 days ago - 19.2 thousand downloads total - 31 stars on GitHub - 1 maintainer
zenith 1.14.0
Gene set analysis following differential expression using linear (mixed) modeling with dream
8 versions - Latest release: 10 days ago - 2 dependent packages - 13.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
hdxmsqc 1.8.0
An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments
6 versions - Latest release: 10 days ago - 4.96 thousand downloads total - 0 stars on GitHub - 1 maintainer
singleCellTK 2.22.0
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
12 versions - Latest release: 10 days ago - 1 dependent package - 41.4 thousand downloads total - 1 maintainer
Top 5.9% on bioconductor.org
systemPipeR 2.18.0
systemPipeR: A Multipurpose Workflow Management System for Reproducible Data Analysis
10 versions - Latest release: 11 days ago - 3 dependent packages - 288 thousand downloads total - 54 stars on GitHub - 1 maintainer
scmeth 1.32.0
Functions to conduct quality control analysis in methylation data
7 versions - Latest release: 11 days ago - 1 dependent package - 16.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
CODEX 1.44.0
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
7 versions - Latest release: 11 days ago - 1 dependent package - 34.6 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
wateRmelon 2.18.0
Illumina DNA methylation array normalization and metrics
7 versions - Latest release: 11 days ago - 5 dependent packages - 187 thousand downloads total - 1 maintainer
systemPipeShiny 1.22.0
systemPipeShiny: An Interactive Framework for Workflow Management and Visualization
7 versions - Latest release: 11 days ago - 12.1 thousand downloads total - 1 maintainer
ENmix 1.48.0
Quality control and analysis tools for Illumina DNA methylation BeadChip
13 versions - Latest release: 11 days ago - 51.4 thousand downloads total - 1 maintainer
EpiCompare 1.16.0
Comparison, Benchmarking & QC of Epigenomic Datasets
16 versions - Latest release: 11 days ago - 8.37 thousand downloads total - 17 stars on GitHub - 1 maintainer
Related Keywords
Software 264 Preprocessing 109 Sequencing 102 Visualization 81 GeneExpression 79 Normalization 75 ImmunoOncology 75 DataImport 73 RNASeq 65 Microarray 61 DifferentialExpression 57 BatchEffect 40 MassSpectrometry 39 Clustering 39 Transcriptomics 39 Proteomics 37 Coverage 36 SingleCell 35 TwoChannel 32 Alignment 30 MultipleComparison 29 DNAMethylation 26 Transcription 25 Genetics 25 OneChannel 21 Regression 21 Epigenetics 20 ChIPSeq 19 GeneSetEnrichment 19 Infrastructure 18 GUI 18 Metabolomics 18 ReportWriting 18 FunctionalGenomics 16 DataRepresentation 16 DimensionReduction 15 bioconductor 15 Classification 15 DifferentialMethylation 14 ShinyApps 13 BiomedicalInformatics 13 r 12 MethylationArray 12 TimeCourse 11 SystemsBiology 11 PrincipalComponent 11 WorkflowStep 11 Bayesian 11 ExperimentalDesign 10 FlowCytometry 10 CellBiology 10 CopyNumberVariation 9 SequenceMatching 8 GeneRegulation 8 ATACSeq 8 Network 8 Spatial 8 mRNAMicroarray 8 Annotation 7 StatisticalMethod 7 MethylSeq 7 CpGIsland 7 AlternativeSplicing 7 DifferentialSplicing 7 GraphAndNetwork 7 Pathways 7 GenomeAnnotation 7 SNP 7 bioconductor-package 6 ProprietaryPlatforms 6 GO 6 CellBasedAssays 6 DNASeq 6 GeneticVariability 6 proteomics 5 AssayDomain 5 FeatureExtraction 5 tidyverse 5 WholeGenome 4 RiboSeq 4 ExonArray 4 CRISPR 4 Cheminformatics 4 shiny 4 Lipidomics 4 MicrotitrePlateAssay 4 qPCR 4 Microbiome 4 MultiChannel 4 bioinformatics 4 mass-spectrometry 4 edger 3 GenomeAssembly 3 deseq2 3 SangerSeq 3 MicroRNAArray 3 MultipleComparisons 3 NucleosomePositioning 3 single-cell 3 genomics 3