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

bioconductor.org "QualityControl" keyword

strandCheckR 1.30.0
Calculate strandness information of a bam file
7 versions - Latest release: 4 months ago - 16.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
ENmix 1.48.3
Quality control and analysis tools for Illumina DNA methylation BeadChip
14 versions - Latest release: about 1 month ago - 54.9 thousand downloads total - 1 maintainer
miRcomp 1.42.0
Tools to assess and compare miRNA expression estimatation methods
8 versions - Latest release: 3 months ago - 23.5 thousand downloads total - 1 maintainer
RNAshapeQC 1.0.0
RNA Coverage-Shape-Based Quality Control Metrics
1 version - Latest release: 4 months ago - 1.26 thousand downloads total - 2 stars on GitHub - 1 maintainer
rnaseqcomp 1.42.0
Benchmarks for RNA-seq Quantification Pipelines
7 versions - Latest release: 2 months ago - 1 dependent package - 23.5 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
wateRmelon 2.18.0
Illumina DNA methylation array normalization and metrics
7 versions - Latest release: 3 months ago - 5 dependent packages - 193 thousand downloads total - 1 maintainer
Guitar 2.28.0
Guitar
7 versions - Latest release: 4 months ago - 35.4 thousand downloads total - 1 maintainer
REMP 1.36.0
Repetitive Element Methylation Prediction
4 versions - Latest release: about 23 hours ago - 22.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
traseR 1.42.0
GWAS trait-associated SNP enrichment analyses in genomic intervals
7 versions - Latest release: 3 months ago - 23.5 thousand downloads total
CellBarcode 1.18.0
Cellular DNA Barcode Analysis toolkit
8 versions - Latest release: 3 months ago - 22.3 thousand downloads total - 2 stars on GitHub - 1 maintainer
GBScleanR 2.6.1
Error correction tool for noisy genotyping by sequencing (GBS) data
14 versions - Latest release: 1 day ago - 11.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
Basic4Cseq 1.48.0
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
7 versions - Latest release: 3 months ago - 34 thousand downloads total - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.40.2
Single-Cell Analysis Toolkit for Gene Expression Data in R
13 versions - Latest release: about 2 months ago - 96 dependent packages - 1.19 million downloads total - 1 maintainer
batchCorr 1.2.0
Within And Between Batch Correction Of LC-MS Metabolomics Data
2 versions - Latest release: 4 months ago - 3.07 thousand downloads total - 0 stars on GitHub - 1 maintainer
MotifPeeker 1.4.0
Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
3 versions - Latest release: 3 months ago - 4.6 thousand downloads total - 2 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: 4 months ago - 14 dependent packages - 439 thousand downloads total - 2 maintainers
stPipe 1.2.0
Upstream pre-processing for Sequencing-Based Spatial Transcriptomics
3 versions - Latest release: 4 months ago - 3.16 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 4.8% on bioconductor.org
affylmGUI 1.86.0
GUI for limma Package with Affymetrix Microarrays
7 versions - Latest release: 3 months ago - 83.6 thousand downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.68.5
Linear Models for Microarray and Omics Data
22 versions - Latest release: 4 days ago - 322 dependent packages - 7.71 million downloads total - 1 maintainer
metaseqR2 1.24.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...
9 versions - Latest release: 3 months ago - 16.4 thousand downloads total - 1 maintainer
qPLEXanalyzer 1.30.0
Tools for quantitative proteomics data analysis
8 versions - Latest release: 4 months ago - 16.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 8.7% on bioconductor.org
regionReport 1.46.0
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
7 versions - Latest release: 4 months ago - 1 dependent package - 41.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
FastqCleaner 1.30.0
A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
7 versions - Latest release: 3 months ago - 1 maintainer
hermes 1.16.0 💰
Preprocessing, analyzing, and reporting of RNA-seq data
9 versions - Latest release: 3 months ago - 15.8 thousand downloads total - 12 stars on GitHub - 1 maintainer
shinyepico 1.20.0
ShinyÉPICo
7 versions - Latest release: 3 months ago - 12.8 thousand downloads total - 5 stars on GitHub - 1 maintainer
lncRna 1.0.0
A Comprehensive Workflow for Long Non-coding RNA Identification and Functional Analysis
1 version - Latest release: 4 months ago - 1.05 thousand downloads total - 7 stars on GitHub - 1 maintainer
yarn 1.38.0
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
7 versions - Latest release: 3 months ago - 1 dependent package - 28.1 thousand downloads total - 1 maintainer
countsimQC 1.30.0
Compare Characteristic Features of Count Data Sets
8 versions - Latest release: 3 months ago - 1 dependent package - 30.7 thousand downloads total - 30 stars on GitHub - 1 maintainer
phenomis 1.14.0
Postprocessing and univariate analysis of omics data
9 versions - Latest release: 3 months ago - 9.64 thousand downloads total - 1 maintainer
MSstatsShiny 1.14.0
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
12 versions - Latest release: 3 months ago - 12.4 thousand downloads total - 9 stars on GitHub - 1 maintainer
MetaProViz 4.0.0
METabolomics pre-PRocessing, functiOnal analysis and VIZualisation
1 version - Latest release: 4 months ago - 1.18 thousand downloads total - 22 stars on GitHub - 1 maintainer
Top 5.6% on bioconductor.org
HTqPCR 1.66.0
Automated analysis of high-throughput qPCR data
7 versions - Latest release: 3 months ago - 2 dependent packages - 65.7 thousand downloads total - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.10.3
Empirical Analysis of Digital Gene Expression Data in R
29 versions - Latest release: 4 days ago - 181 dependent packages - 4.61 million downloads total - 4 maintainers
CytoPipelineGUI 1.10.0
GUI's for visualization of flow cytometry data analysis pipelines
6 versions - Latest release: 3 months ago - 7.88 thousand downloads total - 2 stars on GitHub - 1 maintainer
unifiedWMWqPCR 1.48.0
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
7 versions - Latest release: 3 months ago - 24.8 thousand downloads total - 1 maintainer
MSstatsBioNet 1.4.1
Network Analysis for MS-based Proteomics Experiments
4 versions - Latest release: 2 months ago - 4.84 thousand downloads total - 2 stars on GitHub - 1 maintainer
ggspavis 1.18.1
Visualization functions for spatial transcriptomics data
12 versions - Latest release: 4 days ago - 1 dependent package - 22.8 thousand downloads total - 5 stars on GitHub - 1 maintainer
BioQC 1.40.0
Detect tissue heterogeneity in expression profiles with gene sets
7 versions - Latest release: 3 months ago - 32.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
MSnbase 2.38.1
Base Functions and Classes for Mass Spectrometry and Proteomics
10 versions - Latest release: 8 days ago - 30 dependent packages - 633 thousand downloads total - 123 stars on GitHub - 1 maintainer
bandle 1.16.0
An R package for the Bayesian analysis of differential subcellular localisation experiments
7 versions - Latest release: 3 months ago - 11.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
proDA 1.26.0
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
8 versions - Latest release: 4 months ago - 1 dependent package - 27.8 thousand downloads total - 16 stars on GitHub - 1 maintainer
BatchSVG 1.4.0
Identify Batch-Biased Spatially Variable Genes
3 versions - Latest release: 4 months ago - 4.48 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.58.0
Analyze Illumina Infinium DNA methylation arrays
9 versions - Latest release: 4 months ago - 31 dependent packages - 990 thousand downloads total - 64 stars on GitHub - 1 maintainer
RcwlPipelines 1.28.0
Bioinformatics pipelines based on Rcwl
8 versions - Latest release: 3 months ago - 1 dependent package - 16.4 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
chipseq 1.62.0
chipseq: A package for analyzing chipseq data
7 versions - Latest release: 3 months ago - 4 dependent packages - 154 thousand downloads total - 1 maintainer
ribosomeProfilingQC 1.24.0
Ribosome Profiling Quality Control
8 versions - Latest release: 2 months ago - 16.4 thousand downloads total - 1 maintainer
esATAC 1.34.0
An Easy-to-use Systematic pipeline for ATACseq data analysis
7 versions - Latest release: 3 months ago - 31.1 thousand downloads total - 23 stars on GitHub - 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: 4 months ago - 10 dependent packages - 419 thousand downloads total - 1 maintainer
MAGAR 1.20.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...
7 versions - Latest release: 4 months ago - 12.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
omXplore 1.6.0
Vizualization tools for 'omics' datasets with R
9 versions - Latest release: 3 months ago - 6.59 thousand downloads total - 0 stars on GitHub - 1 maintainer
DegNorm 1.22.0
DegNorm: degradation normalization for RNA-seq data
7 versions - Latest release: 3 months ago - 14 thousand downloads total - 1 stars on GitHub - 1 maintainer
tidyomics 1.8.0
Easily install and load the tidyomics ecosystem
6 versions - Latest release: 4 months ago - 7.57 thousand downloads total - 75 stars on GitHub - 1 maintainer
MSstatsLiP 1.18.0
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
11 versions - Latest release: 6 days ago - 12.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
MBECS 1.16.0
Evaluation and correction of batch effects in microbiome data-sets
7 versions - Latest release: 3 months ago - 12.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
recoup 1.40.0
An R package for the creation of complex genomic profile plots
8 versions - Latest release: 3 months ago - 23.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
MDSvis 1.0.0
Plots of Multi Dimensional Scaling (MDS) results
1 version - Latest release: 4 months ago - 1.08 thousand downloads total - 0 stars on GitHub - 1 maintainer
standR 1.16.0
Spatial transcriptome analyses of Nanostring's DSP data in R
7 versions - Latest release: 4 months ago - 15.6 thousand downloads total - 26 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
EDASeq 2.46.0
Exploratory Data Analysis and Normalization for RNA-Seq
7 versions - Latest release: 3 months ago - 12 dependent packages - 420 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
OLIN 1.90.0
Optimized local intensity-dependent normalisation of two-color microarrays
7 versions - Latest release: 3 months ago - 2 dependent packages - 45.1 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: 3 months ago - 17.8 thousand downloads total - 1 maintainer
ideal 2.6.0
Interactive Differential Expression AnaLysis
7 versions - Latest release: 3 months ago - 27.5 thousand downloads total - 29 stars on GitHub - 1 maintainer
BatchQC 2.8.0
Batch Effects Quality Control Software
8 versions - Latest release: 3 months ago - 33.7 thousand downloads total - 11 stars on GitHub - 1 maintainer
CytoMDS 1.8.0
Low Dimensions projection of cytometry samples
6 versions - Latest release: 3 months ago - 7.6 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 months ago - 2.85 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 9.3% on bioconductor.org
flowClean 1.50.0
flowClean
7 versions - Latest release: 3 months ago - 42.9 thousand downloads total - 1 maintainer
qcmetrics 1.50.0
A Framework for Quality Control
8 versions - Latest release: 3 months ago - 1 dependent package - 33 thousand downloads total - 2 stars on GitHub - 1 maintainer
fraq 1.0.0
A High-Throughput and Extensible Toolkit for Processing FASTQ Data
1 version - Latest release: 4 months ago - 1.17 thousand downloads total - 1 stars on GitHub - 1 maintainer
variancePartition 1.42.0
Quantify and interpret drivers of variation in multilevel gene expression experiments
13 versions - Latest release: 4 months ago - 4 dependent packages - 156 thousand downloads total - 16 stars on GitHub - 1 maintainer
affyPLM 1.88.0
Methods for fitting probe-level models
7 versions - Latest release: 3 months ago - 9 dependent packages - 648 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.70.0
FASTQ input and manipulation
8 versions - Latest release: 4 months ago - 36 dependent packages - 2.05 million downloads total - 1 maintainer
marr 1.22.0
Maximum rank reproducibility
7 versions - Latest release: 3 months ago - 12.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
scds 2.0.0
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
8 versions - Latest release: 3 months ago - 2 dependent packages - 69.7 thousand downloads total - 1 maintainer
scmeth 1.32.0
Functions to conduct quality control analysis in methylation data
7 versions - Latest release: 3 months ago - 1 dependent package - 18.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
notameStats 1.2.0
Workflow for non-targeted LC-MS metabolic profiling
2 versions - Latest release: 3 months ago - 2.26 thousand downloads total - 0 stars on GitHub - 1 maintainer
ATACseqQC 1.36.1
ATAC-seq Quality Control
8 versions - Latest release: 8 days ago - 2 dependent packages - 71.7 thousand downloads total - 1 maintainer
iasva 1.30.0
Iteratively Adjusted Surrogate Variable Analysis
7 versions - Latest release: 3 months ago - 16.9 thousand downloads total - 2 maintainers
alevinQC 1.28.0
Generate QC Reports For Alevin Output
8 versions - Latest release: 3 months ago - 20.9 thousand downloads total - 31 stars on GitHub - 1 maintainer
CytoPipeline 1.12.0
Automation and visualization of flow cytometry data analysis pipelines
7 versions - Latest release: 3 months ago - 2 dependent packages - 10.4 thousand downloads total - 7 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: 3 months ago - 1 dependent package - 93.6 thousand downloads total - 44 stars on GitHub - 1 maintainer
scrapper 1.6.3
Bindings to C++ Libraries for Single-Cell Analysis
7 versions - Latest release: 3 months ago - 38.9 thousand downloads total - 8 stars on GitHub - 1 maintainer
SCOPE 1.24.0
A normalization and copy number estimation method for single-cell DNA sequencing
7 versions - Latest release: 3 months ago - 14.5 thousand downloads total - 1 maintainer
Top 4.2% on bioconductor.org
piano 2.28.0
Platform for integrative analysis of omics data
7 versions - Latest release: 3 months ago - 3 dependent packages - 113 thousand downloads total - 1 maintainer
ibh 1.60.0
Interaction Based Homogeneity for Evaluating Gene Lists
7 versions - Latest release: 3 months ago - 32 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
RnBeads 2.30.0
RnBeads
7 versions - Latest release: 3 months ago - 1 dependent package - 86.3 thousand downloads total - 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: 3 months ago - 14.4 thousand downloads total - 1 maintainer
chevreulShiny 1.4.0
Tools for managing SingleCellExperiment objects as projects
4 versions - Latest release: 3 months ago - 4.51 thousand downloads total - 0 stars on GitHub - 1 maintainer
basecallQC 1.35.0
Working with Illumina Basecalling and Demultiplexing input and output files
7 versions - Latest release: 4 months ago - 21.2 thousand downloads total - 1 maintainer
FilterFFPE 1.22.0
FFPE Artificial Chimeric Read Filter for NGS data
7 versions - Latest release: 2 months ago - 12.7 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
ChIPQC 1.48.3
Quality metrics for ChIPseq data
8 versions - Latest release: 2 months ago - 81.8 thousand downloads total - 2 maintainers
SpaceTrooper 1.2.0
SpaceTrooper performs Quality Control analysis of Image-Based spatial
3 versions - Latest release: 3 months ago - 3.95 thousand downloads total - 11 stars on GitHub - 1 maintainer
seahtrue 1.6.0
Seahtrue revives XF data for structured data analysis
4 versions - Latest release: 4 months ago - 0 stars on GitHub - 1 maintainer
systemPipeTools 1.20.0
Tools for data visualization
7 versions - Latest release: 3 months ago - 11.1 thousand downloads total - 1 maintainer
ppcseq 1.20.0
Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models
7 versions - Latest release: 3 months ago - 11.3 thousand downloads total - 8 stars on GitHub - 1 maintainer
PeacoQC 1.22.0
Peak-based selection of high quality cytometry data
7 versions - Latest release: 3 months ago - 1 dependent package - 24.1 thousand downloads total - 14 stars on GitHub - 1 maintainer
Aerith 1.0.1
visualization and annotation of isotopic enrichment patterns of peptides and metabolites with sta...
2 versions - Latest release: 2 months ago - 1.72 thousand downloads total - 5 stars on GitHub - 1 maintainer
DAPAR 1.44.0
Tools for the Differential Analysis of Proteins Abundance with R
12 versions - Latest release: 3 months ago - 1 dependent package - 34.2 thousand downloads total - 1 maintainer
BERT 1.8.0
High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batc...
5 versions - Latest release: 4 months ago - 6.7 thousand downloads total - 4 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: 3 months ago - 14.6 thousand downloads total - 1 maintainer
Top 5.2% on bioconductor.org
pRoloc 1.52.0
A unifying bioinformatics framework for spatial proteomics
9 versions - Latest release: 3 months ago - 3 dependent packages - 90.2 thousand downloads total - 16 stars on GitHub - 1 maintainer
Scale4C 1.34.0
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
7 versions - Latest release: 4 months ago - 18 thousand downloads total - 1 maintainer
Related Keywords
Software 264 Preprocessing 109 Sequencing 102 Visualization 81 GeneExpression 80 ImmunoOncology 75 Normalization 75 DataImport 73 RNASeq 65 Microarray 61 DifferentialExpression 57 BatchEffect 40 Transcriptomics 39 Clustering 39 MassSpectrometry 39 Proteomics 37 Coverage 36 SingleCell 35 TwoChannel 32 Alignment 30 MultipleComparison 29 DNAMethylation 26 Transcription 25 Genetics 25 Regression 21 OneChannel 21 Epigenetics 20 GeneSetEnrichment 19 ChIPSeq 19 GUI 18 Metabolomics 18 ReportWriting 18 Infrastructure 18 bioconductor 17 DataRepresentation 16 FunctionalGenomics 16 Classification 15 DimensionReduction 15 DifferentialMethylation 14 BiomedicalInformatics 13 ShinyApps 13 MethylationArray 12 r 12 SystemsBiology 11 WorkflowStep 11 Bayesian 11 PrincipalComponent 11 TimeCourse 11 FlowCytometry 10 ExperimentalDesign 10 CellBiology 10 CopyNumberVariation 9 mRNAMicroarray 8 Network 8 SequenceMatching 8 GeneRegulation 8 ATACSeq 8 Spatial 8 MethylSeq 7 AlternativeSplicing 7 DifferentialSplicing 7 SNP 7 CpGIsland 7 GraphAndNetwork 7 Pathways 7 GenomeAnnotation 7 StatisticalMethod 7 Annotation 7 ProprietaryPlatforms 6 proteomics 6 DNASeq 6 bioconductor-package 6 CellBasedAssays 6 GO 6 GeneticVariability 6 FeatureExtraction 5 mass-spectrometry 5 shiny 5 tidyverse 5 AssayDomain 5 r-package 4 MicrotitrePlateAssay 4 CRISPR 4 MultiChannel 4 ExonArray 4 bioinformatics 4 WholeGenome 4 RiboSeq 4 rstats 4 Microbiome 4 qPCR 4 Cheminformatics 4 Lipidomics 4 NetworkEnrichment 3 visualisation 3 NucleosomePositioning 3 single-cell 3 HighThroughputSequencing 3 GenomeAssembly 3 Phylogenetics 3