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

bioconductor.org "QualityControl" keyword

marr 1.20.0
Maximum rank reproducibility
6 versions - Latest release: 5 months ago - 10 thousand downloads total - 2 stars on GitHub - 1 maintainer
arrayMvout 1.68.0
multivariate outlier detection for expression array QA
6 versions - Latest release: 4 months ago - 46.3 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.62.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
6 versions - Latest release: 5 months ago - 10 dependent packages - 409 thousand downloads total - 1 maintainer
pmp 1.22.1
Peak Matrix Processing and signal batch correction for metabolomics datasets
7 versions - Latest release: 5 months ago - 2 dependent packages - 17.5 thousand downloads total - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.8.2
Empirical Analysis of Digital Gene Expression Data in R
26 versions - Latest release: 3 months ago - 181 dependent packages - 4.32 million downloads total - 4 maintainers
Top 1.8% on bioconductor.org
Rsubread 2.24.0
Mapping, quantification and variant analysis of sequencing data
8 versions - Latest release: 5 months ago - 14 dependent packages - 421 thousand downloads total - 2 maintainers
DiscoRhythm 1.26.0
Interactive Workflow for Discovering Rhythmicity in Biological Data
6 versions - Latest release: 5 months ago - 14.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
MSnbase 2.36.0
Base Functions and Classes for Mass Spectrometry and Proteomics
8 versions - Latest release: 5 months ago - 30 dependent packages - 599 thousand downloads total - 123 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.56.0
Analyze Illumina Infinium DNA methylation arrays
8 versions - Latest release: 5 months ago - 31 dependent packages - 950 thousand downloads total - 63 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.38.1
Single-Cell Analysis Toolkit for Gene Expression Data in R
10 versions - Latest release: 12 days ago - 96 dependent packages - 1.08 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.68.0
FASTQ input and manipulation
7 versions - Latest release: 5 months ago - 36 dependent packages - 1.99 million downloads total - 1 maintainer
Top 5.4% on bioconductor.org
QDNAseq 1.46.0
Quantitative DNA Sequencing for Chromosomal Aberrations
6 versions - Latest release: 4 months ago - 4 dependent packages - 79.5 thousand downloads total - 52 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.66.0
Linear Models for Microarray and Omics Data
16 versions - Latest release: 5 months ago - 322 dependent packages - 7.04 million downloads total - 1 maintainer
ngsReports 2.12.1
Load FastqQC reports and other NGS related files
8 versions - Latest release: 4 months ago - 16.6 thousand downloads total - 23 stars on GitHub - 1 maintainer
Top 2.0% on bioconductor.org
monocle 2.38.0
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
7 versions - Latest release: 5 months ago - 6 dependent packages - 496 thousand downloads total - 1 maintainer
Top 0.4% on bioconductor.org
Rsamtools 2.22.0
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
4 versions - Latest release: over 1 year ago - 212 dependent packages - 4.22 million downloads total - 1 maintainer
MSstatsShiny 1.12.1
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
11 versions - Latest release: about 1 month ago - 10.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
abseqR 1.28.0
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
6 versions - Latest release: 4 months ago - 16.2 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
wateRmelon 2.16.0
Illumina DNA methylation array normalization and metrics
6 versions - Latest release: 5 months ago - 5 dependent packages - 184 thousand downloads total - 1 maintainer
qsea 1.36.0
IP-seq data analysis and vizualization
6 versions - Latest release: 5 months ago - 19.2 thousand downloads total - 1 maintainer
Omixer 1.20.0
Omixer: multivariate and reproducible sample randomization to proactively counter batch effects i...
6 versions - Latest release: 5 months ago - 10.2 thousand downloads total - 1 maintainer
strandCheckR 1.28.0
Calculate strandness information of a bam file
6 versions - Latest release: 5 months ago - 13.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
ideal 2.4.0
Interactive Differential Expression AnaLysis
6 versions - Latest release: 5 months ago - 23.8 thousand downloads total - 29 stars on GitHub - 1 maintainer
REMP 1.28.0
Repetitive Element Methylation Prediction
3 versions - Latest release: almost 2 years ago - 12.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
erccdashboard 1.44.0
Assess Differential Gene Expression Experiments with ERCC Controls
6 versions - Latest release: 5 months ago - 27.7 thousand downloads total - 7 stars on GitHub - 1 maintainer
seqTools 1.44.0
Analysis of nucleotide, sequence and quality content on fastq files
6 versions - Latest release: 4 months ago - 1 dependent package - 29 thousand downloads total - 1 maintainer
systemPipeTools 1.18.0
Tools for data visualization
6 versions - Latest release: 5 months ago - 8.9 thousand downloads total - 1 maintainer
scruff 1.28.0
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
7 versions - Latest release: 5 months ago - 15.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
iCheck 1.40.0
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
6 versions - Latest release: 4 months ago - 20.3 thousand downloads total - 1 maintainer
FastqCleaner 1.28.0
A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
6 versions - Latest release: 4 months ago - 17.4 thousand downloads total - 1 maintainer
DOtools 1.0.2
Convenient functions to streamline your single cell data analysis workflow
2 versions - Latest release: about 1 month ago - 1.05 thousand downloads total - 2 stars on GitHub - 1 maintainer
synlet 2.10.0
Hits Selection for Synthetic Lethal RNAi Screen Data
6 versions - Latest release: 5 months ago - 18 thousand downloads total - 1 maintainer
standR 1.14.0
Spatial transcriptome analyses of Nanostring's DSP data in R
6 versions - Latest release: 5 months ago - 12.7 thousand downloads total - 22 stars on GitHub - 1 maintainer
Top 8.8% on bioconductor.org
OLINgui 1.84.0
Graphical user interface for OLIN
6 versions - Latest release: 4 months ago - 37.9 thousand downloads total - 1 maintainer
pvac 1.58.0
PCA-based gene filtering for Affymetrix arrays
6 versions - Latest release: 5 months ago - 32.3 thousand downloads total - 2 maintainers
Top 8.3% on bioconductor.org
MANOR 1.82.0
CGH Micro-Array NORmalization
6 versions - Latest release: 5 months ago - 40.9 thousand downloads total - 1 maintainer
EpiCompare 1.14.0
Comparison, Benchmarking & QC of Epigenomic Datasets
15 versions - Latest release: 4 months ago - 7.55 thousand downloads total - 17 stars on GitHub - 1 maintainer
BatchSVG 1.2.0
Identify Batch-Biased Features in Spatially Variable Genes
2 versions - Latest release: 4 months ago - 3.08 thousand downloads total - 3 stars on GitHub - 1 maintainer
MSstatsLiP 1.16.0
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
10 versions - Latest release: 5 months ago - 10.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
qPLEXanalyzer 1.28.2
Tools for quantitative proteomics data analysis
7 versions - Latest release: about 1 month ago - 14.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
cogeqc 1.14.1
Systematic quality checks on comparative genomics analyses
8 versions - Latest release: 8 days ago - 9.32 thousand downloads total - 8 stars on GitHub - 1 maintainer
OSAT 1.58.0
OSAT: Optimal Sample Assignment Tool
6 versions - Latest release: 4 months ago - 30.4 thousand downloads total - 1 maintainer
basecallQC 1.34.0
Working with Illumina Basecalling and Demultiplexing input and output files
6 versions - Latest release: 4 months ago - 19.1 thousand downloads total - 1 maintainer
Top 8.7% on bioconductor.org
regionReport 1.44.0
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
6 versions - Latest release: 4 months ago - 1 dependent package - 37.9 thousand downloads total - 10 stars on GitHub - 1 maintainer
proDA 1.24.0
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
7 versions - Latest release: 5 months ago - 1 dependent package - 24 thousand downloads total - 16 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
flowAI 1.40.0
Automatic and interactive quality control for flow cytometry data
6 versions - Latest release: 4 months ago - 1 dependent package - 76.6 thousand downloads total - 1 maintainer
squallms 1.4.0
Speedy quality assurance via lasso labeling for LC-MS data
3 versions - Latest release: 4 months ago - 3.87 thousand downloads total - 3 stars on GitHub - 1 maintainer
SmartPhos 1.0.0
A phosphoproteomics data analysis package with an interactive ShinyApp
1 version - Latest release: 5 months ago - 408 downloads total - 5 stars on GitHub - 1 maintainer
omicsGMF 1.0.0
Dimensionality reduction of (single-cell) omics data in R using omicsGMF
1 version - Latest release: 5 months ago - 1.02 thousand downloads total - 1 maintainer
conumee 1.44.0
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
6 versions - Latest release: 4 months ago - 37.9 thousand downloads total - 1 maintainer
SpaceTrooper 1.0.1
SpaceTrooper performs Quality Control analysis of Image-Based spatial
2 versions - Latest release: 3 months ago - 2.14 thousand downloads total - 8 stars on GitHub - 1 maintainer
omXplore 1.4.2
Vizualization tools for 'omics' datasets with R
8 versions - Latest release: 4 months ago - 5.33 thousand downloads total - 0 stars on GitHub - 1 maintainer
gCrisprTools 2.16.0
Suite of Functions for Pooled Crispr Screen QC and Analysis
6 versions - Latest release: 4 months ago - 19.7 thousand downloads total - 1 maintainer
recoup 1.38.0
An R package for the creation of complex genomic profile plots
6 versions - Latest release: 4 months ago - 19.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
doppelgangR 1.38.0
Identify likely duplicate samples from genomic or meta-data
7 versions - Latest release: 4 months ago - 21.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
spiky 1.16.0
Spike-in calibration for cell-free MeDIP
6 versions - Latest release: 4 months ago - 8.62 thousand downloads total - 3 stars on GitHub - 1 maintainer
BERT 1.6.0
High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batc...
4 versions - Latest release: 4 months ago - 5.19 thousand downloads total - 4 stars on GitHub - 1 maintainer
GladiaTOX 1.26.0
R Package for Processing High Content Screening data
8 versions - Latest release: 4 months ago - 11.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
MBECS 1.14.0
Evaluation and correction of batch effects in microbiome data-sets
6 versions - Latest release: 4 months ago - 10.4 thousand downloads total - 4 stars on GitHub - 1 maintainer
tidySingleCellExperiment 1.20.1
Brings SingleCellExperiment to the Tidyverse
7 versions - Latest release: 4 months ago - 4 dependent packages - 22.1 thousand downloads total - 36 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
isobar 1.56.0
Analysis and quantitation of isobarically tagged MSMS proteomics data
6 versions - Latest release: 4 months ago - 45.2 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
segmentSeq 2.44.0
Methods for identifying small RNA loci from high-throughput sequencing data
6 versions - Latest release: 4 months ago - 45.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
MSstatsQCgui 1.30.0
A graphical user interface for MSstatsQC package
6 versions - Latest release: 5 months ago - 13 thousand downloads total - 1 maintainer
CytoPipelineGUI 1.8.0
GUI's for visualization of flow cytometry data analysis pipelines
5 versions - Latest release: 4 months ago - 5.82 thousand downloads total - 2 stars on GitHub - 1 maintainer
GBScleanR 2.4.5
Error correction tool for noisy genotyping by sequencing (GBS) data
12 versions - Latest release: about 1 month ago - 8.99 thousand downloads total - 4 stars on GitHub - 1 maintainer
ERSSA 1.28.0
Empirical RNA-seq Sample Size Analysis
6 versions - Latest release: 4 months ago - 13.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.9% on bioconductor.org
RPA 1.66.0
RPA: Robust Probabilistic Averaging for probe-level analysis
6 versions - Latest release: 5 months ago - 1 dependent package - 39.5 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
interactiveDisplay 1.48.0
Package for enabling powerful shiny web displays of Bioconductor objects
6 versions - Latest release: 4 months ago - 1 dependent package - 58.3 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
DMRcate 3.6.0
Methylation array and sequencing spatial analysis methods
14 versions - Latest release: 4 months ago - 2 dependent packages - 199 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
Rqc 1.44.0
Quality Control Tool for High-Throughput Sequencing Data
6 versions - Latest release: 4 months ago - 48.2 thousand downloads total - 0 stars on GitHub - 1 maintainer
seahtrue 1.4.0
Seahtrue revives XF data for structured data analysis
3 versions - Latest release: 4 months ago - 4.19 thousand downloads total - 0 stars on GitHub - 1 maintainer
BatchQC 2.6.1
Batch Effects Quality Control Software
7 versions - Latest release: about 1 month ago - 30.4 thousand downloads total - 9 stars on GitHub - 1 maintainer
UMI4Cats 1.20.0
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
8 versions - Latest release: 4 months ago - 10.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
scPipe 2.10.0
Pipeline for single cell multi-omic data pre-processing
6 versions - Latest release: 4 months ago - 25.8 thousand downloads total - 69 stars on GitHub - 1 maintainer
KnowSeq 1.24.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
6 versions - Latest release: 4 months ago - 14.3 thousand downloads total - 1 maintainer
statTarget 1.40.0
Statistical Analysis of Molecular Profiles
6 versions - Latest release: 4 months ago - 31.7 thousand downloads total - 1 maintainer
lipidr 2.24.0
Data Mining and Analysis of Lipidomics Datasets
7 versions - Latest release: 4 months ago - 1 dependent package - 19.2 thousand downloads total - 31 stars on GitHub - 1 maintainer
scifer 1.12.0
Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences
7 versions - Latest release: 4 months ago - 7.57 thousand downloads total - 5 stars on GitHub - 1 maintainer
CuratedAtlasQueryR 1.8.0
Queries the Human Cell Atlas
6 versions - Latest release: 4 months ago - 6.94 thousand downloads total - 92 stars on GitHub - 1 maintainer
airpart 1.18.0
Differential cell-type-specific allelic imbalance
6 versions - Latest release: 4 months ago - 11.7 thousand downloads total - 2 stars on GitHub - 1 maintainer
ATACseqQC 1.34.0
ATAC-seq Quality Control
6 versions - Latest release: 4 months ago - 2 dependent packages - 66.5 thousand downloads total - 1 maintainer
MAGAR 1.18.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...
6 versions - Latest release: 4 months ago - 10.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
shinyMethyl 1.46.0
Interactive visualization for Illumina methylation arrays
6 versions - Latest release: 4 months ago - 35.9 thousand downloads total - 6 stars on GitHub - 1 maintainer
esATAC 1.32.0
An Easy-to-use Systematic pipeline for ATACseq data analysis
6 versions - Latest release: 4 months ago - 27.4 thousand downloads total - 23 stars on GitHub - 1 maintainer
Top 3.4% on bioconductor.org
QuasR 1.50.0
Quantify and Annotate Short Reads in R
7 versions - Latest release: 4 months ago - 2 dependent packages - 115 thousand downloads total - 1 maintainer
MSstatsBioNet 1.2.0
Network Analysis for MS-based Proteomics Experiments
2 versions - Latest release: 4 months ago - 3.13 thousand downloads total - 2 stars on GitHub - 1 maintainer
notameViz 1.0.2
Workflow for non-targeted LC-MS metabolic profiling
2 versions - Latest release: about 1 month ago - 1.34 thousand downloads total - 0 stars on GitHub - 1 maintainer
metaseqR2 1.22.1
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...
7 versions - Latest release: 16 days ago - 12.7 thousand downloads total - 1 maintainer
phenomis 1.12.0
Postprocessing and univariate analysis of omics data
8 versions - Latest release: 4 months ago - 7.78 thousand downloads total - 1 maintainer
CaMutQC 1.6.0
An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations
7 versions - Latest release: 4 months ago - 5.46 thousand downloads total - 7 stars on GitHub - 1 maintainer
Guitar 2.26.0
Guitar
6 versions - Latest release: 4 months ago - 31.4 thousand downloads total - 1 maintainer
stPipe 1.0.1
Upstream pre-processing for Sequencing-Based Spatial Transcriptomics
2 versions - Latest release: 4 months ago - 1.49 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
OLIN 1.88.0
Optimized local intensity-dependent normalisation of two-color microarrays
6 versions - Latest release: 4 months ago - 2 dependent packages - 41.1 thousand downloads total - 1 maintainer
ChromSCape 1.20.0
Analysis of single-cell epigenomics datasets with a Shiny App
6 versions - Latest release: 4 months ago - 10.6 thousand downloads total - 14 stars on GitHub - 1 maintainer
rnaseqcomp 1.40.0
Benchmarks for RNA-seq Quantification Pipelines
6 versions - Latest release: 4 months ago - 1 dependent package - 20.5 thousand downloads total - 8 stars on GitHub - 1 maintainer
notameStats 1.0.0
Workflow for non-targeted LC-MS metabolic profiling
1 version - Latest release: 5 months ago - 804 downloads total - 0 stars on GitHub - 1 maintainer
ribosomeProfilingQC 1.22.0
Ribosome Profiling Quality Control
7 versions - Latest release: 4 months ago - 13 thousand downloads total - 1 maintainer
variancePartition 1.40.1
Quantify and interpret drivers of variation in multilevel gene expression experiments
12 versions - Latest release: 3 months ago - 4 dependent packages - 135 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 9.1% on bioconductor.org
spikeLI 2.70.0
Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
6 versions - Latest release: 4 months ago - 33.7 thousand downloads total - 1 maintainer
Spaniel 1.24.0
Spatial Transcriptomics Analysis
6 versions - Latest release: 4 months ago - 13.3 thousand downloads total - 1 maintainer
Related Keywords
Software 255 Preprocessing 108 Sequencing 100 GeneExpression 77 Visualization 76 ImmunoOncology 75 Normalization 74 DataImport 72 RNASeq 63 Microarray 61 DifferentialExpression 56 BatchEffect 40 MassSpectrometry 38 Clustering 38 Transcriptomics 36 SingleCell 35 Coverage 35 Proteomics 35 TwoChannel 32 Alignment 29 MultipleComparison 28 DNAMethylation 26 Genetics 25 Transcription 24 OneChannel 21 Regression 20 GeneSetEnrichment 19 Epigenetics 19 ChIPSeq 19 ReportWriting 18 GUI 18 Infrastructure 17 DataRepresentation 16 Metabolomics 16 FunctionalGenomics 15 bioconductor 15 DimensionReduction 14 ShinyApps 13 Classification 13 BiomedicalInformatics 13 DifferentialMethylation 13 MethylationArray 12 r 12 Bayesian 11 PrincipalComponent 11 TimeCourse 11 ExperimentalDesign 10 CellBiology 10 SystemsBiology 10 CopyNumberVariation 9 WorkflowStep 9 GeneRegulation 8 ATACSeq 8 Network 8 FlowCytometry 8 mRNAMicroarray 8 SequenceMatching 8 AlternativeSplicing 7 CpGIsland 7 GenomeAnnotation 7 MethylSeq 7 DifferentialSplicing 7 Spatial 7 SNP 7 GeneticVariability 6 StatisticalMethod 6 ProprietaryPlatforms 6 Annotation 6 CellBasedAssays 6 bioconductor-package 6 Pathways 6 GO 6 GraphAndNetwork 6 FeatureExtraction 5 AssayDomain 5 tidyverse 5 DNASeq 5 proteomics 5 ExonArray 4 Cheminformatics 4 qPCR 4 MultiChannel 4 MicrotitrePlateAssay 4 WholeGenome 4 RiboSeq 4 shiny 4 bioinformatics 4 Microbiome 4 Lipidomics 4 CRISPR 4 mass-spectrometry 4 deseq2 3 rstats 3 GenomeAssembly 3 r-package 3 transcriptomics 3 edger 3 rnaseq 3 KEGG 3 NetworkEnrichment 3