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

bioconductor.org "Preprocessing" keyword

Top 1.7% on bioconductor.org
sva 3.58.0
Surrogate Variable Analysis
7 versions - Latest release: 6 months ago - 43 dependent packages - 1.2 million downloads total - 3 maintainers
Top 9.9% on bioconductor.org
tilingArray 1.88.0
Transcript mapping with high-density oligonucleotide tiling arrays
6 versions - Latest release: 5 months ago - 2 dependent packages - 62.5 thousand downloads total - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.88.0
Methods for Affymetrix Oligonucleotide Arrays
6 versions - Latest release: 6 months ago - 74 dependent packages - 2.27 million 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: 6 months ago - 10 dependent packages - 410 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: 6 months ago - 14 dependent packages - 423 thousand downloads total - 2 maintainers
Top 1.5% on bioconductor.org
scater 1.38.1
Single-Cell Analysis Toolkit for Gene Expression Data in R
10 versions - Latest release: 23 days ago - 96 dependent packages - 1.09 million downloads total - 1 maintainer
yarn 1.36.0
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
6 versions - Latest release: 5 months ago - 1 dependent package - 25.3 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
vsn 3.78.1
Variance stabilization and calibration for microarray data
7 versions - Latest release: 3 months ago - 30 dependent packages - 1.19 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: 5 months ago - 31 dependent packages - 954 thousand downloads total - 63 stars on GitHub - 1 maintainer
Top 6.9% on bioconductor.org
HTSFilter 1.50.0
Filter replicated high-throughput transcriptome sequencing data
6 versions - Latest release: 5 months ago - 1 dependent package - 62.1 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: 5 months ago - 322 dependent packages - 7.07 million downloads total - 1 maintainer
Top 7.3% on bioconductor.org
TCGAutils 1.30.3
TCGA utility functions for data management
9 versions - Latest release: 2 days ago - 7 dependent packages - 187 thousand downloads total - 19 stars on GitHub - 1 maintainer
EpiMix 1.12.0
EpiMix: an integrative tool for the population-level analysis of DNA methylation
6 versions - Latest release: 5 months ago - 1 dependent package - 8.15 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 10.0% on bioconductor.org
CAGEr 2.16.0
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcr...
6 versions - Latest release: 5 months ago - 2 dependent packages - 48.9 thousand downloads total - 1 maintainer
MetaCyto 1.32.0
MetaCyto: A package for meta-analysis of cytometry data
6 versions - Latest release: 5 months ago - 17.9 thousand downloads total - 1 maintainer
randRotation 1.22.0
Random Rotation Methods for High Dimensional Data with Batch Structure
6 versions - Latest release: 5 months ago - 9.97 thousand downloads total - 0 stars on GitHub - 1 maintainer
matter 2.12.0
Out-of-core statistical computing and signal processing
10 versions - Latest release: 5 months ago - 2 dependent packages - 38.8 thousand downloads total - 52 stars on GitHub - 1 maintainer
miRNAmeConverter 1.38.0
Convert miRNA Names to Different miRBase Versions
6 versions - Latest release: 5 months ago - 18.7 thousand downloads total - 1 maintainer
notame 1.0.1
Workflow for non-targeted LC-MS metabolic profiling
2 versions - Latest release: 3 months ago - 1.86 thousand downloads total - 3 stars on GitHub - 1 maintainer
roastgsa 1.8.0
Rotation based gene set analysis
5 versions - Latest release: 5 months ago - 6.34 thousand downloads total - 0 stars on GitHub - 1 maintainer
gDNAx 1.8.2
Diagnostics for assessing genomic DNA contamination in RNA-seq data
11 versions - Latest release: 4 months ago - 7.32 thousand downloads total - 1 stars on GitHub - 1 maintainer
chevreulProcess 1.2.0
Tools for managing SingleCellExperiment objects as projects
2 versions - Latest release: 5 months ago - 3.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
chevreulShiny 1.2.0
Tools for managing SingleCellExperiment objects as projects
3 versions - Latest release: 4 months ago - 3.02 thousand downloads total - 0 stars on GitHub - 1 maintainer
affyPLM 1.86.0
Methods for fitting probe-level models
6 versions - Latest release: 5 months ago - 9 dependent packages - 638 thousand downloads total - 0 stars on GitHub - 1 maintainer
Prostar 1.42.0
Provides a GUI for DAPAR
12 versions - Latest release: 5 months ago - 26.8 thousand downloads total - 1 maintainer
Top 2.2% on bioconductor.org
marray 1.88.0
Exploratory analysis for two-color spotted microarray data
6 versions - Latest release: 5 months ago - 21 dependent packages - 658 thousand downloads total - 1 maintainer
sangeranalyseR 1.20.0
sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
6 versions - Latest release: 5 months ago - 23.4 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
aroma.light 3.40.0
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Da...
6 versions - Latest release: 5 months ago - 3 dependent packages - 423 thousand downloads total - 1 stars on GitHub - 1 maintainer
scmeth 1.30.0
Functions to conduct quality control analysis in methylation data
6 versions - Latest release: 5 months ago - 1 dependent package - 16.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
scQTLtools 1.2.4
scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of singl...
6 versions - Latest release: about 1 month ago - 2.89 thousand downloads total - 5 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: 5 months ago - 39.8 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
multiscan 1.70.0
R package for combining multiple scans
6 versions - Latest release: 5 months ago - 35.4 thousand downloads total - 1 maintainer
mobileRNA 1.6.2
mobileRNA: Investigate the RNA mobilome & population-scale changes
10 versions - Latest release: about 1 month ago - 5.89 thousand downloads total - 1 maintainer
Top 3.6% on bioconductor.org
ballgown 2.42.0
Flexible, isoform-level differential expression analysis
6 versions - Latest release: 5 months ago - 3 dependent packages - 221 thousand downloads total - 141 stars on GitHub - 1 maintainer
transformGamPoi 1.16.0
Variance Stabilizing Transformation for Gamma-Poisson Models
6 versions - Latest release: 5 months ago - 9.85 thousand downloads total - 22 stars on GitHub - 1 maintainer
BUS 1.66.0
Gene network reconstruction
6 versions - Latest release: 5 months ago - 37 thousand downloads total - 1 maintainer
DspikeIn 1.0.0
Estimating Absolute Abundance from Microbial Spike-in Controls
2 versions - Latest release: 4 months ago - 1.29 thousand downloads total - 16 stars on GitHub - 1 maintainer
rgoslin 1.14.0
Lipid Shorthand Name Parsing and Normalization
6 versions - Latest release: 5 months ago - 11.1 thousand downloads total - 6 stars on GitHub - 1 maintainer
BreastSubtypeR 1.2.0
Cohort-aware methods for intrinsic molecular subtyping of breast cancer
2 versions - Latest release: 5 months ago - 3.23 thousand downloads total - 3 stars on GitHub - 1 maintainer
zenith 1.12.0
Gene set analysis following differential expression using linear (mixed) modeling with dream
7 versions - Latest release: 5 months ago - 2 dependent packages - 13 thousand downloads total - 0 stars on GitHub - 1 maintainer
ExiMiR 2.52.0
R functions for the normalization of Exiqon miRNA array data
6 versions - Latest release: 5 months ago - 34.6 thousand downloads total - 1 maintainer
MiChip 1.64.0
MiChip Parsing and Summarizing Functions
6 versions - Latest release: 5 months ago - 33.9 thousand downloads total - 1 maintainer
nondetects 2.40.0
Non-detects in qPCR data
7 versions - Latest release: 5 months ago - 25.6 thousand downloads total - 1 maintainer
epimutacions 1.14.0
Robust outlier identification for DNA methylation data
7 versions - Latest release: 5 months ago - 9.01 thousand downloads total - 0 stars on GitHub - 1 maintainer
sights 1.36.0
Statistics and dIagnostic Graphs for HTS
6 versions - Latest release: 5 months ago - 17.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
SWATH2stats 1.40.1
Transform and Filter SWATH Data for Statistical Packages
8 versions - Latest release: 2 months ago - 22.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
cellity 1.38.0
Quality Control for Single-Cell RNA-seq Data
6 versions - Latest release: 5 months ago - 21.5 thousand downloads total - 1 maintainer
RcwlPipelines 1.26.0
Bioinformatics pipelines based on Rcwl
7 versions - Latest release: 5 months ago - 1 dependent package - 14.6 thousand downloads total - 1 maintainer
primirTSS 1.28.0
Prediction of pri-miRNA Transcription Start Site
6 versions - Latest release: 5 months ago - 12.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
piano 2.26.0
Platform for integrative analysis of omics data
6 versions - Latest release: 5 months ago - 3 dependent packages - 107 thousand downloads total - 1 maintainer
Doscheda 1.32.0
A DownStream Chemo-Proteomics Analysis Pipeline
6 versions - Latest release: 5 months ago - 16.6 thousand downloads total - 1 maintainer
iasva 1.28.0
Iteratively Adjusted Surrogate Variable Analysis
6 versions - Latest release: 5 months ago - 14.8 thousand downloads total - 2 maintainers
Top 8.8% on bioconductor.org
nnNorm 2.74.0
Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
6 versions - Latest release: 5 months ago - 38.2 thousand downloads total - 1 maintainer
tRNAscanImport 1.30.0
Importing a tRNAscan-SE result file as GRanges object
6 versions - Latest release: 5 months ago - 2 dependent packages - 15.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
scuttle 1.20.0
Single-Cell RNA-Seq Analysis Utilities
6 versions - Latest release: 5 months ago - 41 dependent packages - 1.11 million downloads total - 1 maintainer
RbowtieCuda 1.2.0
An R Wrapper for nvBowtie and nvBWT, a rewritten version of Bowtie2 for cuda
5 versions - Latest release: 5 months ago - 2.37 thousand downloads total - 2 stars on GitHub - 1 maintainer
Harman 1.38.0
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
6 versions - Latest release: 5 months ago - 1 dependent package - 31.8 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
a4Preproc 1.58.0
Automated Affymetrix Array Analysis Preprocessing Package
6 versions - Latest release: 5 months ago - 4 dependent packages - 57.8 thousand downloads total - 1 maintainer
Top 7.8% on bioconductor.org
AgiMicroRna 2.60.0
Processing and Differential Expression Analysis of Agilent microRNA chips
6 versions - Latest release: 5 months ago - 60.9 thousand downloads total - 1 maintainer
GOTHiC 1.46.0
Binomial test for Hi-C data analysis
6 versions - Latest release: 5 months ago - 33 thousand downloads total - 1 maintainer
Top 5.6% on bioconductor.org
HTqPCR 1.64.0
Automated analysis of high-throughput qPCR data
6 versions - Latest release: 5 months ago - 2 dependent packages - 62.3 thousand downloads total - 1 maintainer
scMitoMut 1.6.0
Single-cell Mitochondrial Mutation Analysis Tool
4 versions - Latest release: 5 months ago - 5.51 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
limmaGUI 1.86.0
GUI for limma Package With Two Color Microarrays
6 versions - Latest release: 5 months ago - 59.2 thousand downloads total - 1 maintainer
AWAggregator 1.0.0
Attribute-Weighted Aggregation
1 version - Latest release: 5 months ago - 1.45 thousand downloads total - 0 stars on GitHub - 1 maintainer
chevreulPlot 1.2.0
Plots used in the chevreulPlot package
2 versions - Latest release: 5 months ago - 3.04 thousand downloads total - 0 stars on GitHub - 1 maintainer
CGHnormaliter 1.64.0
Normalization of array CGH data with imbalanced aberrations.
6 versions - Latest release: 5 months ago - 37.2 thousand downloads total - 1 maintainer
crumblr 1.2.0
Count ratio uncertainty modeling base linear regression
2 versions - Latest release: 5 months ago - 3.11 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
EDASeq 2.44.0
Exploratory Data Analysis and Normalization for RNA-Seq
6 versions - Latest release: 5 months ago - 12 dependent packages - 408 thousand downloads total - 5 stars on GitHub - 1 maintainer
ptairMS 1.18.0
Pre-processing PTR-TOF-MS Data
6 versions - Latest release: 5 months ago - 10.2 thousand downloads total - 7 stars on GitHub - 1 maintainer
NTW 1.60.0
Predict gene network using an Ordinary Differential Equation (ODE) based method
6 versions - Latest release: 5 months ago - 29.4 thousand downloads total - 1 maintainer
scFeatureFilter 1.30.1
A correlation-based method for quality filtering of single-cell RNAseq data
7 versions - Latest release: about 1 month ago - 14.4 thousand downloads total - 1 maintainer
SIAMCAT 2.14.0
Statistical Inference of Associations between Microbial Communities And host phenoTypes
6 versions - Latest release: 5 months ago - 22.5 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: 5 months ago - 38.7 thousand downloads total - 1 maintainer
ABarray 1.78.0
Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1...
6 versions - Latest release: 5 months ago - 55.4 thousand downloads total - 1 maintainer
Top 3.7% on bioconductor.org
DEGseq 1.64.0
Identify Differentially Expressed Genes from RNA-seq data
6 versions - Latest release: 5 months ago - 112 thousand downloads total - 1 maintainer
R4RNA 1.38.0
An R package for RNA visualization and analysis
6 versions - Latest release: 5 months ago - 2 dependent packages - 59.1 thousand downloads total - 1 maintainer
bigmelon 1.36.0
Illumina methylation array analysis for large experiments
6 versions - Latest release: 5 months ago - 23.1 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
RnBeads 2.28.0
RnBeads
6 versions - Latest release: 5 months ago - 1 dependent package - 81.9 thousand downloads total - 1 maintainer
MACSQuantifyR 1.24.0
Fast treatment of MACSQuantify FACS data
6 versions - Latest release: 5 months ago - 10.1 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
REDseq 1.56.0
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
6 versions - Latest release: 5 months ago - 40.6 thousand downloads total - 1 maintainer
Top 8.7% on bioconductor.org
genArise 1.86.0
Microarray Analysis tool
6 versions - Latest release: 5 months ago - 38.3 thousand downloads total - 1 maintainer
Top 7.3% on bioconductor.org
r3Cseq 1.56.0
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
6 versions - Latest release: 5 months ago - 45.2 thousand downloads total - 1 maintainer
megadepth 1.20.0
megadepth: BigWig and BAM related utilities
6 versions - Latest release: 5 months ago - 2 dependent packages - 17.2 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 3.4% on bioconductor.org
Mfuzz 2.70.0
Soft clustering of omics time series data
6 versions - Latest release: 5 months ago - 5 dependent packages - 183 thousand downloads total - 1 maintainer
PeacoQC 1.20.0
Peak-based selection of high quality cytometry data
6 versions - Latest release: 5 months ago - 1 dependent package - 20.7 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
GreyListChIP 1.42.0
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
6 versions - Latest release: 5 months ago - 2 dependent packages - 131 thousand downloads total - 1 maintainer
proActiv 1.20.0
Estimate Promoter Activity from RNA-Seq data
6 versions - Latest release: 5 months ago - 13.1 thousand downloads total - 53 stars on GitHub - 1 maintainer
Top 6.6% on bioconductor.org
methylumi 2.56.0
Handle Illumina methylation data
6 versions - Latest release: 5 months ago - 7 dependent packages - 393 thousand downloads total - 8 stars on GitHub - 1 maintainer
PepsNMR 1.28.0
Pre-process 1H-NMR FID signals
6 versions - Latest release: 5 months ago - 1 dependent package - 21 thousand downloads total - 8 stars on GitHub - 1 maintainer
DEqMS 1.28.0
a tool to perform statistical analysis of differential protein expression for quantitative proteo...
6 versions - Latest release: 5 months ago - 30.5 thousand downloads total - 17 stars on GitHub - 1 maintainer
ARRmNormalization 1.50.0
Adaptive Robust Regression normalization for Illumina methylation data
6 versions - Latest release: 5 months ago - 31 thousand downloads total - 1 maintainer
nnSVG 1.14.0
Scalable identification of spatially variable genes in spatially-resolved transcriptomics data
10 versions - Latest release: 5 months ago - 2 dependent packages - 12.6 thousand downloads total - 22 stars on GitHub - 1 maintainer
dreamlet 1.8.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...
7 versions - Latest release: 5 months ago - 10.2 thousand downloads total - 20 stars on GitHub - 1 maintainer
ramwas 1.34.0
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
6 versions - Latest release: 5 months ago - 21.8 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
affycomp 1.86.0
Graphics Toolbox for Assessment of Affymetrix Expression Measures
6 versions - Latest release: 5 months ago - 71.5 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
stepNorm 1.82.0
Stepwise normalization functions for cDNA microarrays
6 versions - Latest release: 5 months ago - 37.3 thousand downloads total - 1 maintainer
peakCombiner 1.0.0
The R package to curate and merge enriched genomic regions into consensus peak sets
1 version - Latest release: 5 months ago - 1.21 thousand downloads total - 1 maintainer
flowGate 1.10.0
Interactive Cytometry Gating in R
6 versions - Latest release: 5 months ago - 8.15 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
frma 1.62.0
Frozen RMA and Barcode
6 versions - Latest release: 5 months ago - 2 dependent packages - 78.5 thousand downloads total - 1 maintainer
spillR 1.6.0
Spillover Compensation in Mass Cytometry Data
6 versions - Latest release: 5 months ago - 5.4 thousand downloads total - 1 maintainer
Related Keywords
Software 290 QualityControl 108 Microarray 90 GeneExpression 90 Normalization 85 Sequencing 82 ImmunoOncology 79 DataImport 71 Visualization 71 RNASeq 68 DifferentialExpression 57 SingleCell 44 Transcriptomics 41 TwoChannel 40 BatchEffect 37 DNAMethylation 34 OneChannel 34 Clustering 33 MassSpectrometry 33 MultipleComparison 32 Regression 29 Proteomics 27 Transcription 25 Coverage 23 Genetics 21 Epigenetics 20 Metabolomics 20 Alignment 19 StatisticalMethod 19 Classification 17 DataRepresentation 16 FunctionalGenomics 15 DimensionReduction 15 GeneSetEnrichment 14 MethylationArray 14 WorkflowStep 13 FlowCytometry 13 Bayesian 13 CopyNumberVariation 13 DifferentialMethylation 12 SNP 11 CellBasedAssays 11 BiomedicalInformatics 11 PrincipalComponent 11 r 11 TimeCourse 10 GeneRegulation 10 GUI 10 ChIPSeq 10 Annotation 10 ExperimentalDesign 10 CpGIsland 9 bioinformatics 9 SystemsBiology 9 GenomeAnnotation 9 bioconductor 8 mRNAMicroarray 8 FeatureExtraction 7 Network 7 bioconductor-package 7 CellBiology 7 Infrastructure 7 DifferentialSplicing 7 AlternativeSplicing 7 GeneticVariability 6 SequenceMatching 6 Pathways 6 ProprietaryPlatforms 6 Spatial 6 ExonArray 6 genomics 6 PeakDetection 5 Cheminformatics 5 ATACSeq 5 rstats 5 GenomeWideAssociation 5 MultiChannel 5 GraphAndNetwork 5 single-cell 5 ReportWriting 5 Lipidomics 4 MethylSeq 4 ChipOnChip 4 ThirdPartyClient 4 r-package 4 ShinyApps 4 rna-seq 4 MicroRNAArray 4 DNASeq 3 MicrotitrePlateAssay 3 BiologicalQuestion 3 qPCR 3 ComparativeGenomics 3 visualization 3 GO 3 Survival 3 DifferentialPeakCalling 3 proteomics 3 WholeGenome 3 GenomicVariation 3