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bioconductor.org "QualityControl" keyword

PeacoQC 1.20.0
Peak-based selection of high quality cytometry data
6 versions - Latest release: 3 months ago - 1 dependent package - 19.9 thousand downloads total - 14 stars on GitHub - 1 maintainer
ramwas 1.34.0
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
6 versions - Latest release: 3 months ago - 21 thousand downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.68.0
FASTQ input and manipulation
7 versions - Latest release: 4 months ago - 36 dependent packages - 1.98 million downloads total - 1 maintainer
Doscheda 1.32.0
A DownStream Chemo-Proteomics Analysis Pipeline
6 versions - Latest release: 3 months ago - 15.9 thousand downloads total - 1 maintainer
Top 5.2% on bioconductor.org
pRoloc 1.50.0
A unifying bioinformatics framework for spatial proteomics
8 versions - Latest release: 4 months ago - 3 dependent packages - 82.6 thousand downloads total - 16 stars on GitHub - 1 maintainer
yarn 1.36.0
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
6 versions - Latest release: 3 months ago - 1 dependent package - 24.4 thousand downloads total - 1 maintainer
TargetDecoy 1.16.0
Diagnostic Plots to Evaluate the Target Decoy Approach
6 versions - Latest release: 3 months ago - 8.71 thousand downloads total - 1 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: 4 months ago - 30 dependent packages - 592 thousand downloads total - 123 stars on GitHub - 1 maintainer
Top 6.6% on bioconductor.org
methylumi 2.56.0
Handle Illumina methylation data
6 versions - Latest release: 4 months ago - 7 dependent packages - 390 thousand downloads total - 8 stars on GitHub - 1 maintainer
RiboProfiling 1.39.1
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
6 versions - Latest release: 3 months ago - 25.9 thousand downloads total - 1 maintainer
miRcomp 1.40.0
Tools to assess and compare miRNA expression estimatation methods
7 versions - Latest release: 4 months ago - 19.6 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
Rsubread 2.24.0
Mapping, quantification and variant analysis of sequencing data
8 versions - Latest release: 4 months ago - 14 dependent packages - 417 thousand downloads total - 2 maintainers
Top 4.7% on bioconductor.org
interactiveDisplayBase 1.48.0
Base package for enabling powerful shiny web displays of Bioconductor objects
6 versions - Latest release: 3 months ago - 3 dependent packages - 1.03 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.56.0
Analyze Illumina Infinium DNA methylation arrays
8 versions - Latest release: 4 months ago - 31 dependent packages - 941 thousand downloads total - 63 stars on GitHub - 1 maintainer
countsimQC 1.28.1
Compare Characteristic Features of Count Data Sets
7 versions - Latest release: about 14 hours ago - 1 dependent package - 24.9 thousand downloads total - 29 stars on GitHub - 1 maintainer
ffpe 1.54.0
Quality assessment and control for FFPE microarray expression data
6 versions - Latest release: 3 months ago - 33.8 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: 4 months ago - 10 dependent packages - 406 thousand downloads total - 1 maintainer
MSstatsQC 2.28.0
Longitudinal system suitability monitoring and quality control for proteomic experiments
6 versions - Latest release: 3 months ago - 1 dependent package - 16.8 thousand downloads total - 1 maintainer
GmicR 1.24.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...
6 versions - Latest release: 3 months ago - 11.8 thousand downloads total - 1 maintainer
AMARETTO 1.26.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...
6 versions - Latest release: 4 months ago - 17.2 thousand downloads total - 1 maintainer
DExMA 1.18.0
Differential Expression Meta-Analysis
7 versions - Latest release: 3 months ago - 9.7 thousand downloads total - 1 maintainer
Top 4.8% on bioconductor.org
affylmGUI 1.84.0
GUI for limma Package with Affymetrix Microarrays
6 versions - Latest release: 3 months ago - 78.5 thousand downloads total - 1 maintainer
CytoPipeline 1.10.0
Automation and visualization of flow cytometry data analysis pipelines
6 versions - Latest release: 3 months ago - 2 dependent packages - 7.71 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.38.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
9 versions - Latest release: 4 months ago - 96 dependent packages - 1.06 million downloads total - 1 maintainer
bigmelon 1.36.0
Illumina methylation array analysis for large experiments
6 versions - Latest release: 3 months ago - 22.3 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
dyebias 1.70.0
The GASSCO method for correcting for slide-dependent gene-specific dye bias
6 versions - Latest release: 3 months ago - 37.7 thousand downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.66.0
Linear Models for Microarray and Omics Data
16 versions - Latest release: 4 months ago - 322 dependent packages - 6.96 million downloads total - 1 maintainer
flowCut 1.20.0
Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis
6 versions - Latest release: 3 months ago - 14.6 thousand downloads total - 1 maintainer
shinyepico 1.18.0
ShinyÉPICo
6 versions - Latest release: 3 months ago - 9.75 thousand downloads total - 5 stars on GitHub - 1 maintainer
ENmix 1.46.1
Quality control and analysis tools for Illumina DNA methylation BeadChip
11 versions - Latest release: 30 days ago - 48.8 thousand downloads total - 1 maintainer
artMS 1.28.0
Analytical R tools for Mass Spectrometry
6 versions - Latest release: 3 months ago - 16.9 thousand downloads total - 1 maintainer
SPIAT 1.12.1
Spatial Image Analysis of Tissues
11 versions - Latest release: 1 day ago - 11.3 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 9.1% on bioconductor.org
Harshlight 1.82.0
A "corrective make-up" program for microarray chips
6 versions - Latest release: 4 months ago - 39 thousand downloads total - 1 maintainer
massiR 1.46.0
massiR: MicroArray Sample Sex Identifier
6 versions - Latest release: 3 months ago - 24.6 thousand downloads total - 1 maintainer
FilterFFPE 1.20.0
FFPE Artificial Chimeric Read Filter for NGS data
6 versions - Latest release: 3 months ago - 9.9 thousand downloads total - 1 maintainer
qckitfastq 1.26.0
FASTQ Quality Control
6 versions - Latest release: 3 months ago - 11.2 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
altcdfenvs 2.72.0
alternative CDF environments (aka probeset mappings)
6 versions - Latest release: 4 months ago - 1 dependent package - 51 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
pcaExplorer 3.4.0
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
6 versions - Latest release: 4 months ago - 2 dependent packages - 67.1 thousand downloads total - 56 stars on GitHub - 1 maintainer
bandle 1.14.0
An R package for the Bayesian analysis of differential subcellular localisation experiments
6 versions - Latest release: 3 months ago - 8.57 thousand downloads total - 4 stars on GitHub - 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: 2 months ago - 181 dependent packages - 4.27 million downloads total - 4 maintainers
Top 4.1% on bioconductor.org
GWASTools 1.56.0
Tools for Genome Wide Association Studies
6 versions - Latest release: 3 months ago - 4 dependent packages - 139 thousand downloads total - 18 stars on GitHub - 1 maintainer
RadioGx 2.14.0
Analysis of Large-Scale Radio-Genomic Data
6 versions - Latest release: 3 months ago - 12.4 thousand downloads total - 1 maintainer
DAPAR 1.42.0
Tools for the Differential Analysis of Proteins Abundance with R
11 versions - Latest release: 3 months ago - 1 dependent package - 30.6 thousand downloads total - 1 maintainer
DegNorm 1.20.0
DegNorm: degradation normalization for RNA-seq data
6 versions - Latest release: 3 months ago - 11.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
dks 1.56.0
The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
6 versions - Latest release: 3 months ago - 27.7 thousand downloads total - 1 maintainer
CellBarcode 1.16.0
Cellular DNA Barcode Analysis toolkit
7 versions - Latest release: 4 months ago - 19.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
CODEX 1.42.0
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
6 versions - Latest release: 3 months ago - 1 dependent package - 33 thousand downloads total - 1 maintainer
Top 5.5% on bioconductor.org
dupRadar 1.40.0
Assessment of duplication rates in RNA-Seq datasets
6 versions - Latest release: 3 months ago - 60.7 thousand downloads total - 2 stars on GitHub - 2 maintainers
MatrixQCvis 1.18.0
Shiny-based interactive data-quality exploration for omics data
6 versions - Latest release: 3 months ago - 11.1 thousand downloads total - 1 maintainer
Top 5.6% on bioconductor.org
sesame 1.28.1
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
9 versions - Latest release: 2 months ago - 4 dependent packages - 90.3 thousand downloads total - 80 stars on GitHub - 1 maintainer
cummeRbund 2.51.0
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
6 versions - Latest release: 3 months ago - 594 thousand downloads total - 1 maintainer
SCOPE 1.22.0
A normalization and copy number estimation method for single-cell DNA sequencing
6 versions - Latest release: 3 months ago - 11.7 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
HELP 1.68.0
Tools for HELP data analysis
6 versions - Latest release: 3 months ago - 37.6 thousand downloads total - 1 maintainer
Top 5.5% on bioconductor.org
MEDIPS 1.62.0
DNA IP-seq data analysis
6 versions - Latest release: 3 months ago - 63 thousand downloads total - 1 maintainer
IONiseR 2.34.0
Quality Assessment Tools for Oxford Nanopore MinION data
6 versions - Latest release: 3 months ago - 27.2 thousand downloads total - 1 maintainer
ChIPexoQual 1.34.0
ChIPexoQual
6 versions - Latest release: 3 months ago - 19.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 9.5% on bioconductor.org
nucleR 2.42.0
Nucleosome positioning package for R
6 versions - Latest release: 3 months ago - 37.1 thousand downloads total - 1 maintainer
alevinQC 1.26.0
Generate QC Reports For Alevin Output
7 versions - Latest release: 4 months ago - 17.2 thousand downloads total - 31 stars on GitHub - 1 maintainer
CytoMDS 1.6.1
Low Dimensions projection of cytometry samples
5 versions - Latest release: 2 months ago - 5.45 thousand downloads total - 1 stars on GitHub - 1 maintainer
miQC 1.18.0
Flexible, probabilistic metrics for quality control of scRNA-seq data
6 versions - Latest release: 3 months ago - 13.9 thousand downloads total - 16 stars on GitHub - 1 maintainer
qcmetrics 1.48.0
A Framework for Quality Control
7 versions - Latest release: 4 months ago - 1 dependent package - 28.7 thousand downloads total - 2 stars on GitHub - 1 maintainer
snm 1.58.0
Supervised Normalization of Microarrays
6 versions - Latest release: 3 months ago - 1 dependent package - 46.1 thousand downloads total - 1 maintainer
AffyRNADegradation 1.56.0
Analyze and correct probe positional bias in microarray data due to RNA degradation
6 versions - Latest release: 3 months ago - 36.1 thousand downloads total - 1 maintainer
singleCellTK 2.20.1
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
11 versions - Latest release: 30 days ago - 1 dependent package - 39.2 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
beadarray 2.60.0
Quality assessment and low-level analysis for Illumina BeadArray data
7 versions - Latest release: 30 days ago - 5 dependent packages - 234 thousand downloads total - 1 maintainer
skewr 1.42.0
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
6 versions - Latest release: 3 months ago - 19 thousand downloads total - 1 maintainer
traseR 1.40.0
GWAS trait-associated SNP enrichment analyses in genomic intervals
6 versions - Latest release: 3 months ago - 19.3 thousand downloads total
sights 1.36.0
Statistics and dIagnostic Graphs for HTS
6 versions - Latest release: 3 months ago - 16.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
ibh 1.58.0
Interaction Based Homogeneity for Evaluating Gene Lists
6 versions - Latest release: 4 months ago - 29.3 thousand downloads total - 1 maintainer
scds 1.26.1
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
7 versions - Latest release: 1 day ago - 2 dependent packages - 60 thousand downloads total - 1 maintainer
scTGIF 1.24.0
Cell type annotation for unannotated single-cell RNA-Seq data
6 versions - Latest release: 3 months ago - 1 dependent package - 14.3 thousand downloads total - 1 maintainer
hermes 1.14.0 💰
Preprocessing, analyzing, and reporting of RNA-seq data
8 versions - Latest release: 4 months ago - 12.3 thousand downloads total - 12 stars on GitHub - 1 maintainer
arrayMvout 1.68.0
multivariate outlier detection for expression array QA
6 versions - Latest release: 4 months ago - 45.4 thousand downloads total - 1 maintainer
marr 1.20.0
Maximum rank reproducibility
6 versions - Latest release: 4 months ago - 9.55 thousand downloads total - 2 stars on GitHub - 1 maintainer
pmp 1.22.1
Peak Matrix Processing and signal batch correction for metabolomics datasets
7 versions - Latest release: 4 months ago - 2 dependent packages - 16.9 thousand downloads total - 1 maintainer
DiscoRhythm 1.26.0
Interactive Workflow for Discovering Rhythmicity in Biological Data
6 versions - Latest release: 4 months ago - 13.9 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
QDNAseq 1.46.0
Quantitative DNA Sequencing for Chromosomal Aberrations
6 versions - Latest release: 3 months ago - 4 dependent packages - 78.2 thousand downloads total - 52 stars on GitHub - 1 maintainer
ngsReports 2.12.1
Load FastqQC reports and other NGS related files
8 versions - Latest release: 3 months ago - 16.1 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: 4 months ago - 6 dependent packages - 489 thousand downloads total - 1 maintainer
MSstatsShiny 1.12.1
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
11 versions - Latest release: 6 days ago - 9.86 thousand downloads total - 9 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: 4 months ago - 5 dependent packages - 182 thousand downloads total - 1 maintainer
scruff 1.28.0
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
7 versions - Latest release: 4 months ago - 14.6 thousand downloads total - 8 stars on GitHub - 1 maintainer
DOtools 1.0.2
Convenient functions to streamline your single cell data analysis workflow
2 versions - Latest release: 7 days ago - 672 downloads total - 2 stars on GitHub - 1 maintainer
pvac 1.58.0
PCA-based gene filtering for Affymetrix arrays
6 versions - Latest release: 4 months ago - 31.7 thousand downloads total - 2 maintainers
BatchSVG 1.2.0
Identify Batch-Biased Features in Spatially Variable Genes
2 versions - Latest release: 3 months ago - 2.83 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 8.3% on bioconductor.org
MANOR 1.82.0
CGH Micro-Array NORmalization
6 versions - Latest release: 4 months ago - 40.1 thousand downloads total - 1 maintainer
DspikeIn 1.0.0
Estimating Absolute Abundance from Microbial Spike-in Controls
2 versions - Latest release: 3 months ago - 843 downloads total - 16 stars on GitHub - 1 maintainer
standR 1.14.0
Spatial transcriptome analyses of Nanostring's DSP data in R
6 versions - Latest release: 4 months ago - 12.1 thousand downloads total - 22 stars on GitHub - 1 maintainer
Omixer 1.20.0
Omixer: multivariate and reproducible sample randomization to proactively counter batch effects i...
6 versions - Latest release: 4 months ago - 9.73 thousand downloads total - 1 maintainer
MSstatsLiP 1.16.0
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
10 versions - Latest release: 4 months ago - 9.69 thousand downloads total - 3 stars on GitHub - 1 maintainer
systemPipeTools 1.18.0
Tools for data visualization
6 versions - Latest release: 4 months ago - 8.47 thousand downloads total - 1 maintainer
erccdashboard 1.44.0
Assess Differential Gene Expression Experiments with ERCC Controls
6 versions - Latest release: 4 months ago - 27 thousand downloads total - 7 stars on GitHub - 1 maintainer
ideal 2.4.0
Interactive Differential Expression AnaLysis
6 versions - Latest release: 4 months ago - 22.9 thousand downloads total - 29 stars on GitHub - 1 maintainer
EpiCompare 1.14.0
Comparison, Benchmarking & QC of Epigenomic Datasets
15 versions - Latest release: 3 months ago - 7.13 thousand downloads total - 17 stars on GitHub - 1 maintainer
qsea 1.36.0
IP-seq data analysis and vizualization
6 versions - Latest release: 4 months ago - 18.4 thousand downloads total - 1 maintainer
SmartPhos 1.0.0
A phosphoproteomics data analysis package with an interactive ShinyApp
1 version - Latest release: 4 months ago - 339 downloads total - 5 stars on GitHub - 1 maintainer
notame 1.0.1
Workflow for non-targeted LC-MS metabolic profiling
2 versions - Latest release: about 1 month ago - 1.43 thousand downloads total - 3 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: 3 months ago - 15.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
FastqCleaner 1.28.0
A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
6 versions - Latest release: 3 months ago - 16.8 thousand downloads total - 1 maintainer
OSAT 1.58.0
OSAT: Optimal Sample Assignment Tool
6 versions - Latest release: 3 months ago - 29.7 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 Clustering 38 MassSpectrometry 38 Transcriptomics 36 Proteomics 35 SingleCell 35 Coverage 35 TwoChannel 32 Alignment 29 MultipleComparison 28 DNAMethylation 26 Genetics 25 Transcription 24 OneChannel 21 Regression 20 GeneSetEnrichment 19 ChIPSeq 19 Epigenetics 19 GUI 18 ReportWriting 18 Infrastructure 17 Metabolomics 16 DataRepresentation 16 FunctionalGenomics 15 bioconductor 15 DimensionReduction 14 Classification 13 ShinyApps 13 DifferentialMethylation 13 BiomedicalInformatics 13 r 12 MethylationArray 12 TimeCourse 11 PrincipalComponent 11 Bayesian 11 CellBiology 10 ExperimentalDesign 10 SystemsBiology 10 WorkflowStep 9 CopyNumberVariation 9 Network 8 FlowCytometry 8 ATACSeq 8 SequenceMatching 8 GeneRegulation 8 mRNAMicroarray 8 AlternativeSplicing 7 Spatial 7 DifferentialSplicing 7 MethylSeq 7 CpGIsland 7 GenomeAnnotation 7 SNP 7 Annotation 6 bioconductor-package 6 CellBasedAssays 6 GeneticVariability 6 StatisticalMethod 6 ProprietaryPlatforms 6 Pathways 6 GraphAndNetwork 6 GO 6 AssayDomain 5 FeatureExtraction 5 proteomics 5 tidyverse 5 DNASeq 5 Lipidomics 4 CRISPR 4 shiny 4 MicrotitrePlateAssay 4 WholeGenome 4 Cheminformatics 4 Microbiome 4 MultiChannel 4 ExonArray 4 qPCR 4 mass-spectrometry 4 bioinformatics 4 RiboSeq 4 SangerSeq 3 MultipleComparisons 3 NucleosomePositioning 3 HighThroughputSequencing 3 Bioinformatics 3 deseq2 3 edger 3 NetworkEnrichment 3 genomics 3