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bioconductor.org "QualityControl" keyword

ramwas 1.36.0
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
7 versions - Latest release: 3 months ago - 1 maintainer
consensus 1.30.0
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
7 versions - Latest release: 3 months ago - 1 maintainer
CaMutQC 1.8.0
An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations
8 versions - Latest release: 2 months ago - 6.31 thousand downloads total - 7 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: 2 months ago - 2 dependent packages - 56 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: 3 months ago - 31 dependent packages - 983 thousand downloads total - 64 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 - 6 stars on GitHub - 1 maintainer
Spaniel 1.26.0
Spatial Transcriptomics Analysis
7 versions - Latest release: about 2 months ago - 15.1 thousand downloads total - 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: 3 months ago - 30 dependent packages - 627 thousand downloads total - 123 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: 3 months ago - 14 dependent packages - 435 thousand downloads total - 2 maintainers
Top 0.6% on bioconductor.org
edgeR 4.10.1
Empirical Analysis of Digital Gene Expression Data in R
28 versions - Latest release: 2 months ago - 181 dependent packages - 4.54 million downloads total - 4 maintainers
doppelgangR 1.38.0
Identify likely duplicate samples from genomic or meta-data
7 versions - Latest release: 8 months ago - 22.6 thousand downloads total - 5 stars on GitHub - 1 maintainer
scruff 1.30.0
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
8 versions - Latest release: 2 months ago - 8 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: 3 months ago - 10 dependent packages - 418 thousand downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.70.0
FASTQ input and manipulation
8 versions - Latest release: 3 months ago - 36 dependent packages - 1 maintainer
mobileRNA 1.8.0
mobileRNA: Investigate the RNA mobilome & population-scale changes
11 versions - Latest release: 2 months ago - 1 maintainer
skewr 1.44.0
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
7 versions - Latest release: 3 months ago - 1 maintainer
SPIAT 1.14.0
Spatial Image Analysis of Tissues
12 versions - Latest release: 3 months ago - 13.2 thousand downloads total - 24 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: 3 months ago - 0 stars on GitHub - 1 maintainer
MatrixQCvis 1.20.0
Shiny-based interactive data-quality exploration for omics data
7 versions - Latest release: 3 months ago - 12.9 thousand downloads total - 1 maintainer
strandCheckR 1.30.0
Calculate strandness information of a bam file
7 versions - Latest release: 3 months ago - 15.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
ffpe 1.56.0
Quality assessment and control for FFPE microarray expression data
7 versions - Latest release: 3 months ago - 1 maintainer
ChromSCape 1.22.0
Analysis of single-cell epigenomics datasets with a Shiny App
7 versions - Latest release: about 2 months ago - 13.2 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 9.1% on bioconductor.org
spikeLI 2.72.0
Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
7 versions - Latest release: 3 months ago - 36.1 thousand downloads total - 1 maintainer
singleCellTK 2.22.0
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
12 versions - Latest release: 3 months ago - 1 dependent package - 43.5 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: 22 days ago - 96 dependent packages - 1.17 million downloads total - 1 maintainer
tidySingleCellExperiment 1.22.0
Brings SingleCellExperiment to the Tidyverse
8 versions - Latest release: 3 months ago - 4 dependent packages - 25.6 thousand downloads total - 36 stars on GitHub - 1 maintainer
systemPipeShiny 1.22.0
systemPipeShiny: An Interactive Framework for Workflow Management and Visualization
7 versions - Latest release: 3 months ago - 13.1 thousand downloads total - 1 maintainer
CytoMDS 1.8.0
Low Dimensions projection of cytometry samples
6 versions - Latest release: 2 months ago - 7.22 thousand downloads total - 1 stars on GitHub - 1 maintainer
scrapper 1.6.3
Bindings to C++ Libraries for Single-Cell Analysis
7 versions - Latest release: about 2 months ago - 28 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
scuttle 1.22.0
Legacy Utilities for Single-Cell RNA-Seq Analysis
7 versions - Latest release: 3 months ago - 41 dependent packages - 1.38 million downloads total - 1 maintainer
conumee 1.46.0
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
7 versions - Latest release: 3 months ago - 40.7 thousand downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.68.4
Linear Models for Microarray and Omics Data
21 versions - Latest release: about 2 months ago - 322 dependent packages - 7.55 million downloads total - 1 maintainer
DExMA 1.20.0
Differential Expression Meta-Analysis
8 versions - Latest release: about 1 month ago - 12 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
Rqc 1.46.0
Quality Control Tool for High-Throughput Sequencing Data
7 versions - Latest release: 3 months ago - 52.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.0% on bioconductor.org
monocle 2.40.0
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
8 versions - Latest release: about 2 months ago - 6 dependent packages - 519 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: 3 months ago - 3 dependent packages - 294 thousand downloads total - 52 stars on GitHub - 1 maintainer
shinyMethyl 1.48.0
Interactive visualization for Illumina methylation arrays
7 versions - Latest release: 2 months ago - 39.2 thousand downloads total - 6 stars on GitHub - 1 maintainer
CompensAID 1.0.0
Automated detection tool for spillover errors
1 version - Latest release: 3 months ago - 1.27 thousand downloads total - 1 maintainer
MWASTools 1.36.0
MWASTools: an integrated pipeline to perform metabolome-wide association studies
7 versions - Latest release: 3 months ago - 1 dependent package - 25.8 thousand downloads total - 2 maintainers
notame 1.2.0
Workflow for non-targeted LC-MS metabolic profiling
3 versions - Latest release: 2 months ago - 2.99 thousand downloads total - 3 stars on GitHub - 1 maintainer
spiky 1.18.0
Spike-in calibration for cell-free MeDIP
7 versions - Latest release: 2 months ago - 10.6 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.1% on bioconductor.org
GWASTools 1.58.0
Tools for Genome Wide Association Studies
7 versions - Latest release: 3 months ago - 4 dependent packages - 149 thousand downloads total - 18 stars on GitHub - 1 maintainer
pmp 1.24.0
Peak Matrix Processing and signal batch correction for metabolomics datasets
8 versions - Latest release: 3 months ago - 2 dependent packages - 19.9 thousand downloads total - 1 maintainer
GloScope 2.2.0
Population-level Representation on scRNA-Seq data
7 versions - Latest release: 2 months ago - 8.08 thousand downloads total - 1 stars on GitHub - 1 maintainer
RadioGx 2.16.0
Analysis of Large-Scale Radio-Genomic Data
7 versions - Latest release: 3 months ago - 14.9 thousand downloads total - 1 maintainer
assorthead 1.6.3
Assorted Header-Only C++ Libraries
6 versions - Latest release: about 1 month ago - 471 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 8.8% on bioconductor.org
OLINgui 1.86.0
Graphical user interface for OLIN
7 versions - Latest release: 3 months ago - 40.1 thousand downloads total - 1 maintainer
synlet 2.12.0
Hits Selection for Synthetic Lethal RNAi Screen Data
7 versions - Latest release: 3 months ago - 19.9 thousand downloads total - 1 maintainer
iCheck 1.42.0
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
7 versions - Latest release: 3 months ago - 22.5 thousand downloads total - 1 maintainer
dreamlet 1.10.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...
8 versions - Latest release: 2 months ago - 12.5 thousand downloads total - 23 stars on GitHub - 1 maintainer
AssessORF 1.30.0
Assess Gene Predictions Using Proteomics and Evolutionary Conservation
7 versions - Latest release: 2 months ago - 19 thousand downloads total - 1 maintainer
Omixer 1.22.0
Omixer: multivariate and reproducible sample randomization to proactively counter batch effects i...
7 versions - Latest release: 3 months ago - 11.8 thousand downloads total - 1 maintainer
OSAT 1.60.0
OSAT: Optimal Sample Assignment Tool
7 versions - Latest release: 2 months ago - 32.6 thousand downloads total - 1 maintainer
squallms 1.6.0
Speedy quality assurance via lasso labeling for LC-MS data
4 versions - Latest release: 3 months ago - 4.51 thousand downloads total - 3 stars on GitHub - 1 maintainer
CuratedAtlasQueryR 1.10.0
Queries the Human Cell Atlas
7 versions - Latest release: 3 months ago - 8.4 thousand downloads total - 93 stars on GitHub - 1 maintainer
CleanUpRNAseq 1.6.0
Detect and Correct Genomic DNA Contamination in RNA-seq Data
4 versions - Latest release: about 2 months ago - 5.7 thousand downloads total - 1 maintainer
cogeqc 1.16.0
Systematic quality checks on comparative genomics analyses
9 versions - Latest release: about 1 month ago - 11.3 thousand downloads total - 8 stars on GitHub - 1 maintainer
ENmix 1.48.3
Quality control and analysis tools for Illumina DNA methylation BeadChip
14 versions - Latest release: 7 days ago - 53.6 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: 3 months ago - 5 dependent packages - 191 thousand downloads total - 1 maintainer
bigmelon 1.38.0
Illumina methylation array analysis for large experiments
7 versions - Latest release: 3 months ago - 25.1 thousand downloads total - 1 maintainer
CODEX 1.44.0
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
7 versions - Latest release: 3 months ago - 1 dependent package - 35.9 thousand downloads total - 1 maintainer
IONiseR 2.35.0
Quality Assessment Tools for Oxford Nanopore MinION data
7 versions - Latest release: 3 months ago - 30 thousand downloads total - 1 maintainer
dks 1.58.0
The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
7 versions - Latest release: 3 months ago - 30 thousand downloads total - 1 maintainer
rnaseqcomp 1.42.0
Benchmarks for RNA-seq Quantification Pipelines
7 versions - Latest release: about 1 month ago - 1 dependent package - 22.8 thousand downloads total - 8 stars on GitHub - 1 maintainer
omicsGMF 1.2.0
Dimensionality reduction of (single-cell) omics data in R using omicsGMF
2 versions - Latest release: 3 months ago - 2.24 thousand 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: 3 months ago - 61.6 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
segmentSeq 2.46.0
Methods for identifying small RNA loci from high-throughput sequencing data
7 versions - Latest release: 3 months ago - 48.9 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 - 4.26 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
QDNAseq 1.48.0
Quantitative DNA Sequencing for Chromosomal Aberrations
7 versions - Latest release: 3 months ago - 4 dependent packages - 83.9 thousand downloads total - 54 stars on GitHub - 1 maintainer
tRanslatome 1.50.0
Comparison between multiple levels of gene expression
7 versions - Latest release: 3 months ago - 32.1 thousand downloads total - 2 maintainers
GBScleanR 2.6.0
Error correction tool for noisy genotyping by sequencing (GBS) data
13 versions - Latest release: 2 months ago - 10.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 8.3% on bioconductor.org
MANOR 1.84.0
CGH Micro-Array NORmalization
7 versions - Latest release: 10 days ago - 43.3 thousand downloads total - 1 maintainer
Top 6.6% on bioconductor.org
methylumi 2.58.0
Handle Illumina methylation data
7 versions - Latest release: 3 months ago - 7 dependent packages - 403 thousand downloads total - 8 stars on GitHub - 1 maintainer
batchCorr 1.2.0
Within And Between Batch Correction Of LC-MS Metabolomics Data
2 versions - Latest release: 3 months ago - 2.73 thousand downloads total - 0 stars on GitHub - 1 maintainer
cummeRbund 2.54.0
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
7 versions - Latest release: 3 months ago - 597 thousand downloads total - 1 maintainer
stPipe 1.2.0
Upstream pre-processing for Sequencing-Based Spatial Transcriptomics
3 versions - Latest release: 3 months ago - 2.84 thousand downloads total - 5 stars on GitHub - 1 maintainer
MSstatsBioNet 1.4.1
Network Analysis for MS-based Proteomics Experiments
4 versions - Latest release: about 2 months ago - 4.47 thousand downloads total - 2 stars on GitHub - 1 maintainer
shinyepico 1.20.0
ShinyÉPICo
7 versions - Latest release: 2 months ago - 12.1 thousand downloads total - 5 stars on GitHub - 1 maintainer
arrayMvout 1.70.0
multivariate outlier detection for expression array QA
7 versions - Latest release: 3 months ago - 48.7 thousand downloads total - 1 maintainer
DegNorm 1.22.0
DegNorm: degradation normalization for RNA-seq data
7 versions - Latest release: 3 months ago - 13.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
miRcomp 1.42.0
Tools to assess and compare miRNA expression estimatation methods
8 versions - Latest release: 3 months ago - 22.5 thousand downloads total - 1 maintainer
ggspavis 1.18.0
Visualization functions for spatial transcriptomics data
11 versions - Latest release: 3 months ago - 1 dependent package - 21.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
proDA 1.26.0
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
8 versions - Latest release: 3 months ago - 1 dependent package - 26.8 thousand downloads total - 16 stars on GitHub - 1 maintainer
standR 1.16.0
Spatial transcriptome analyses of Nanostring's DSP data in R
7 versions - Latest release: 3 months ago - 15.1 thousand downloads total - 23 stars on GitHub - 1 maintainer
MSstatsShiny 1.14.0
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
12 versions - Latest release: 3 months ago - 11.9 thousand downloads total - 9 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 - 64.7 thousand downloads total - 1 maintainer
MetaProViz 4.0.0
METabolomics pre-PRocessing, functiOnal analysis and VIZualisation
1 version - Latest release: 3 months ago - 762 downloads total - 1 maintainer
Top 5.7% on bioconductor.org
flowAI 1.42.0
Automatic and interactive quality control for flow cytometry data
7 versions - Latest release: about 2 months ago - 1 dependent package - 80.7 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: 3 months ago - 12.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.6% on bioconductor.org
sesame 1.30.1
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
11 versions - Latest release: 14 days ago - 4 dependent packages - 98.8 thousand downloads total - 80 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: about 2 months ago - 12 dependent packages - 417 thousand downloads total - 5 stars on GitHub - 1 maintainer
sights 1.38.0
Statistics and dIagnostic Graphs for HTS
7 versions - Latest release: 2 months ago - 18.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
ribosomeProfilingQC 1.24.0
Ribosome Profiling Quality Control
8 versions - Latest release: about 2 months ago - 15.7 thousand downloads total - 1 maintainer
recoup 1.40.0
An R package for the creation of complex genomic profile plots
8 versions - Latest release: about 2 months ago - 22.9 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: 3 months ago - 4 dependent packages - 151 thousand downloads total - 16 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: 3 months ago - 1 dependent package - 40.7 thousand downloads total - 10 stars on GitHub - 1 maintainer
RNAshapeQC 1.0.0
RNA Coverage-Shape-Based Quality Control Metrics
1 version - Latest release: 3 months ago - 896 downloads total - 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 - 67.8 thousand downloads total - 1 maintainer
tidyomics 1.8.0
Easily install and load the tidyomics ecosystem
6 versions - Latest release: 3 months ago - 7.21 thousand downloads total - 75 stars on GitHub - 1 maintainer
Top 9.3% on bioconductor.org
flowClean 1.50.0
flowClean
7 versions - Latest release: 3 months ago - 42.2 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 Clustering 39 Transcriptomics 39 MassSpectrometry 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 Metabolomics 18 GUI 18 ReportWriting 18 Infrastructure 18 FunctionalGenomics 16 DataRepresentation 16 bioconductor 16 DimensionReduction 15 Classification 15 DifferentialMethylation 14 BiomedicalInformatics 13 ShinyApps 13 r 12 MethylationArray 12 PrincipalComponent 11 Bayesian 11 SystemsBiology 11 TimeCourse 11 WorkflowStep 11 FlowCytometry 10 ExperimentalDesign 10 CellBiology 10 CopyNumberVariation 9 ATACSeq 8 Network 8 GeneRegulation 8 Spatial 8 SequenceMatching 8 mRNAMicroarray 8 StatisticalMethod 7 DifferentialSplicing 7 MethylSeq 7 AlternativeSplicing 7 Pathways 7 SNP 7 CpGIsland 7 GenomeAnnotation 7 GraphAndNetwork 7 Annotation 7 GO 6 DNASeq 6 bioconductor-package 6 CellBasedAssays 6 ProprietaryPlatforms 6 GeneticVariability 6 AssayDomain 5 FeatureExtraction 5 tidyverse 5 proteomics 5 r-package 4 qPCR 4 Lipidomics 4 RiboSeq 4 shiny 4 MultiChannel 4 MicrotitrePlateAssay 4 bioinformatics 4 mass-spectrometry 4 CRISPR 4 WholeGenome 4 Microbiome 4 ExonArray 4 Cheminformatics 4 MultidimensionalScaling 3 rstats 3 Phylogenetics 3 MicroRNAArray 3 Bioinformatics 3 ComparativeGenomics 3 KEGG 3 NucleosomePositioning 3