Ecosyste.ms: Packages

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

bioconductor.org "Preprocessing" keyword

Top 1.9% on bioconductor.org
minfi 1.50.0
Analyze Illumina Infinium DNA methylation arrays
3 versions - Latest release: about 1 month ago - 31 dependent packages - 789 thousand downloads total - 58 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.56.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
3 versions - Latest release: 28 days ago - 10 dependent packages - 336 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
Rsubread 2.18.0
Mapping, quantification and variant analysis of sequencing data
4 versions - Latest release: 28 days ago - 14 dependent packages - 313 thousand downloads total - 2 maintainers
MungeSumstats 1.12.0
Standardise summary statistics from GWAS
4 versions - Latest release: about 1 month ago - 24.4 thousand downloads total - 64 stars on GitHub - 1 maintainer
AlpsNMR 4.6.0
Automated spectraL Processing System for NMR
3 versions - Latest release: 27 days ago - 5.05 thousand downloads total - 13 stars on GitHub - 1 maintainer
spillR 0.99.10
Spillover Compensation in Mass Cytometry Data
2 versions - Latest release: about 1 month ago - 392 downloads total - 1 maintainer
scMitoMut 1.0.0
Single-cell Mitochondrial Mutation Analysis Tool
1 version - Latest release: about 1 month ago - 380 downloads total - 0 stars on GitHub - 1 maintainer
spoon 0.99.10
Address the Mean-variance Relationship in Spatial Transcriptomics Data
2 versions - Latest release: about 1 month ago - 292 downloads total - 0 stars on GitHub - 1 maintainer
tpSVG 0.99.7
Thin plate models to detect spatially variable genes
2 versions - Latest release: about 1 month ago - 292 downloads total - 0 stars on GitHub - 1 maintainer
BERT 1.0.0
Hierarchical Batch-Effect Adjustment with Trees
1 version - Latest release: about 1 month ago - 377 downloads total - 2 stars on GitHub - 1 maintainer
mobileRNA 1.0.0
mobileRNA: Investigate the RNA mobilome & population-scale changes
2 versions - Latest release: about 1 month ago - 405 downloads total - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.32.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
4 versions - Latest release: about 1 month ago - 96 dependent packages - 625 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
vsn 3.72.0
Variance stabilization and calibration for microarray data
3 versions - Latest release: about 1 month ago - 30 dependent packages - 896 thousand downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.60.0
Linear Models for Microarray Data
5 versions - Latest release: about 1 month ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.52.0
Surrogate Variable Analysis
3 versions - Latest release: about 1 month ago - 43 dependent packages - 808 thousand downloads total - 3 maintainers
Top 0.9% on bioconductor.org
affy 1.82.0
Methods for Affymetrix Oligonucleotide Arrays
3 versions - Latest release: about 1 month ago - 74 dependent packages - 1.86 million downloads total - 1 maintainer
tRNAscanImport 1.22.0
Importing a tRNAscan-SE result file as GRanges object
3 versions - Latest release: 6 months ago - 2 dependent packages - 7.99 thousand downloads total - 2 stars on GitHub - 1 maintainer
BEclear 2.18.0
Correction of batch effects in DNA methylation data
3 versions - Latest release: 7 months ago - 15.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
dreamlet 1.2.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...
3 versions - Latest release: 28 days ago - 1.3 thousand downloads total - 9 stars on GitHub - 1 maintainer
demuxmix 1.4.0
Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models
3 versions - Latest release: 7 months ago - 1 dependent package - 4.55 thousand downloads total - 4 stars on GitHub - 1 maintainer
DEsingle 1.22.0
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
3 versions - Latest release: 6 months ago - 1 dependent package - 24.1 thousand downloads total - 29 stars on GitHub - 1 maintainer
hermes 1.6.1 💰
Preprocessing, analyzing, and reporting of RNA-seq data
4 versions - Latest release: about 2 months ago - 3.31 thousand downloads total - 11 stars on GitHub - 1 maintainer
ChromSCape 1.12.0
Analysis of single-cell epigenomics datasets with a Shiny App
3 versions - Latest release: 7 months ago - 4.34 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
gcrma 2.74.0
Background Adjustment Using Sequence Information
3 versions - Latest release: 7 months ago - 9 dependent packages - 618 thousand downloads total - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis
2 versions - Latest release: 7 months ago - 881 downloads total - 0 stars on GitHub - 1 maintainer
CytoPipeline 1.4.0
Automation and visualization of flow cytometry data analysis pipelines
3 versions - Latest release: 24 days ago - 2 dependent packages - 1.97 thousand downloads total - 3 stars on GitHub - 1 maintainer
primirTSS 1.20.0
Prediction of pri-miRNA Transcription Start Site
3 versions - Latest release: 6 months ago - 5.92 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
biovizBase 1.50.0
Basic graphic utilities for visualization of genomic data.
3 versions - Latest release: 7 months ago - 17 dependent packages - 1.05 million downloads total - 1 maintainer
MEAT 1.14.0
Muscle Epigenetic Age Test
3 versions - Latest release: 6 months ago - 4.53 thousand downloads total - 0 stars on GitHub - 1 maintainer
qPLEXanalyzer 1.20.0
Tools for quantitative proteomics data analysis
3 versions - Latest release: 6 months ago - 7.02 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
marray 1.80.0
Exploratory analysis for two-color spotted microarray data
3 versions - Latest release: 7 months ago - 21 dependent packages - 550 thousand downloads total - 1 maintainer
shinyMethyl 1.38.0
Interactive visualization for Illumina methylation arrays
3 versions - Latest release: 6 months ago - 24.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
DNABarcodeCompatibility 1.18.0
A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Genera...
3 versions - Latest release: 6 months ago - 5.27 thousand downloads total - 7 stars on GitHub - 1 maintainer
PepsNMR 1.20.0
Pre-process 1H-NMR FID signals
3 versions - Latest release: 6 months ago - 1 dependent package - 9.18 thousand downloads total - 10 stars on GitHub - 1 maintainer
CluMSID 1.18.0
Clustering of MS2 Spectra for Metabolite Identification
3 versions - Latest release: 6 months ago - 6.85 thousand downloads total - 9 stars on GitHub - 1 maintainer
CytoPipelineGUI 1.0.0
GUI's for visualization of flow cytometry data analysis pipelines
2 versions - Latest release: 7 months ago - 921 downloads total - 0 stars on GitHub - 1 maintainer
protGear 1.6.0
Protein Micro Array Data Management and Interactive Visualization
3 versions - Latest release: 7 months ago - 2.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.3% on bioconductor.org
TCGAutils 1.22.2
TCGA utility functions for data management
4 versions - Latest release: 5 months ago - 7 dependent packages - 60.8 thousand downloads total - 19 stars on GitHub - 1 maintainer
scmeth 1.22.0
Functions to conduct quality control analysis in methylation data
3 versions - Latest release: 6 months ago - 1 dependent package - 8.27 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
scuttle 1.12.0
Single-Cell RNA-Seq Analysis Utilities
3 versions - Latest release: 7 months ago - 41 dependent packages - 548 thousand downloads total - 1 maintainer
affyPLM 1.78.0
Methods for fitting probe-level models
3 versions - Latest release: 7 months ago - 9 dependent packages - 569 thousand downloads total - 0 stars on GitHub - 1 maintainer
REMP 1.26.0
Repetitive Element Methylation Prediction
3 versions - Latest release: 6 months ago - 11.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
rCGH 1.32.0
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
3 versions - Latest release: 6 months ago - 1 dependent package - 16 thousand downloads total - 4 stars on GitHub - 1 maintainer
CAGEfightR 1.22.0
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
3 versions - Latest release: 6 months ago - 1 dependent package - 18.7 thousand downloads total - 8 stars on GitHub - 1 maintainer
scruff 1.20.0
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
3 versions - Latest release: 6 months ago - 7.81 thousand downloads total - 8 stars on GitHub - 1 maintainer
PeacoQC 1.12.0
Peak-based selection of high quality cytometry data
3 versions - Latest release: 6 months ago - 1 dependent package - 7.69 thousand downloads total - 14 stars on GitHub - 1 maintainer
MAGAR 1.10.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...
3 versions - Latest release: 7 months ago - 4.57 thousand downloads total - 0 stars on GitHub - 1 maintainer
scCB2 1.12.0
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
3 versions - Latest release: 6 months ago - 3.98 thousand downloads total - 10 stars on GitHub - 1 maintainer
scifer 1.4.0
Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences
3 versions - Latest release: 7 months ago - 1.72 thousand downloads total - 5 stars on GitHub - 1 maintainer
bnbc 1.24.2
Bandwise normalization and batch correction of Hi-C data
4 versions - Latest release: 3 months ago - 9.61 thousand downloads total - 1 stars on GitHub - 1 maintainer
orthogene 1.8.0
Interspecies gene mapping
3 versions - Latest release: 7 months ago - 1 dependent package - 10.4 thousand downloads total - 35 stars on GitHub - 1 maintainer
ReUseData 1.2.2
Reusable and reproducible Data Management
5 versions - Latest release: 5 months ago - 1.11 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
tximport 1.30.0
Import and summarize transcript-level estimates for transcript- and gene-level analysis
3 versions - Latest release: 7 months ago - 13 dependent packages - 360 thousand downloads total - 130 stars on GitHub - 1 maintainer
RNAinteract 1.50.0
Estimate Pairwise Interactions from multidimensional features
3 versions - Latest release: 7 months ago - 23.7 thousand downloads total - 1 maintainer
covEB 1.28.0
Empirical Bayes estimate of block diagonal covariance matrices
3 versions - Latest release: 7 months ago - 9.93 thousand downloads total - 1 maintainer
UMI4Cats 1.12.0
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
3 versions - Latest release: 7 months ago - 3.93 thousand downloads total - 4 stars on GitHub - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data
4 versions - Latest release: 26 days ago - 3.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
gemma.R 3.0.3
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...
6 versions - Latest release: 18 days ago - 2.01 thousand downloads total - 9 stars on GitHub - 1 maintainer
matter 2.6.1
Scientific computing for out-of-memory signals and images
5 versions - Latest release: 21 days ago - 2 dependent packages - 19 thousand downloads total - 52 stars on GitHub - 1 maintainer
Top 5.6% on bioconductor.org
sesame 1.22.0
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
3 versions - Latest release: 22 days ago - 4 dependent packages - 50.3 thousand downloads total - 48 stars on GitHub - 1 maintainer
Top 6.6% on bioconductor.org
methylumi 2.48.0
Handle Illumina methylation data
3 versions - Latest release: 7 months ago - 7 dependent packages - 296 thousand downloads total - 8 stars on GitHub - 1 maintainer
shinyepico 1.10.0
ShinyÉPICo
3 versions - Latest release: 7 months ago - 3.54 thousand downloads total - 3 stars on GitHub - 1 maintainer
SynMut 1.18.0
SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures
3 versions - Latest release: 7 months ago - 5.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
GGPA 1.14.0
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architec...
3 versions - Latest release: 7 months ago - 4.23 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 8.1% on bioconductor.org
maigesPack 1.66.0
Functions to handle cDNA microarray data, including several methods of data analysis
3 versions - Latest release: 7 months ago - 30.1 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
altcdfenvs 2.64.0
alternative CDF environments (aka probeset mappings)
3 versions - Latest release: 7 months ago - 1 dependent package - 39.6 thousand downloads total - 1 maintainer
Top 8.0% on bioconductor.org
OLIN 1.80.0
Optimized local intensity-dependent normalisation of two-color microarrays
3 versions - Latest release: 7 months ago - 2 dependent packages - 31 thousand downloads total - 1 maintainer
megadepth 1.12.0
megadepth: BigWig and BAM related utilities
3 versions - Latest release: 7 months ago - 2 dependent packages - 6.86 thousand downloads total - 11 stars on GitHub - 1 maintainer
BatchQC 1.30.0
Batch Effects Quality Control Software
3 versions - Latest release: 6 months ago - 20.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
IRISFGM 1.10.0
Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq
3 versions - Latest release: 7 months ago - 3 thousand downloads total - 1 maintainer
CGHnormaliter 1.56.0
Normalization of array CGH data with imbalanced aberrations.
3 versions - Latest release: 7 months ago - 28.1 thousand downloads total - 1 maintainer
crossmeta 1.28.0
Cross Platform Meta-Analysis of Microarray Data
3 versions - Latest release: 6 months ago - 1 dependent package - 15.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.9% on bioconductor.org
RPA 1.58.0
RPA: Robust Probabilistic Averaging for probe-level analysis
3 versions - Latest release: 7 months ago - 1 dependent package - 30.5 thousand downloads total - 1 maintainer
IsoCorrectoR 1.20.0
Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isoto...
3 versions - Latest release: 7 months ago - 1 dependent package - 7.23 thousand downloads total - 1 maintainer
Top 7.0% on bioconductor.org
SCAN.UPC 2.44.0
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
3 versions - Latest release: 7 months ago - 35.2 thousand downloads total - 1 maintainer
IsoCorrectoRGUI 1.18.0
Graphical User Interface for IsoCorrectoR
3 versions - Latest release: 7 months ago - 1 dependent package - 5.43 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
quantro 1.36.0
A test for when to use quantile normalization
3 versions - Latest release: 7 months ago - 3 dependent packages - 32.9 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
REDseq 1.48.0
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
3 versions - Latest release: 7 months ago - 31.3 thousand downloads total - 1 maintainer
conumee 1.36.0
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
3 versions - Latest release: 7 months ago - 23.8 thousand downloads total - 1 maintainer
flowGate 1.2.0
Interactive Cytometry Gating in R
3 versions - Latest release: 7 months ago - 1.55 thousand downloads total - 1 maintainer
CONSTANd 1.10.0
Data normalization by matrix raking
3 versions - Latest release: 7 months ago - 3.41 thousand downloads total - 1 maintainer
Top 7.4% on bioconductor.org
RefPlus 1.72.0
A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
3 versions - Latest release: 7 months ago - 31.9 thousand downloads total - 1 maintainer
MBQN 2.14.0
Mean/Median-balanced quantile normalization
3 versions - Latest release: 7 months ago - 4.27 thousand downloads total - 2 stars on GitHub - 1 maintainer
gespeR 1.34.0
Gene-Specific Phenotype EstimatoR
3 versions - Latest release: 7 months ago - 16.3 thousand downloads total - 1 maintainer
diffHic 1.34.0
Differential Analysis of Hi-C Data
3 versions - Latest release: 7 months ago - 22.9 thousand downloads total - 3 maintainers
Top 8.2% on bioconductor.org
qpcrNorm 1.60.0
Data-driven normalization strategies for high-throughput qPCR data.
3 versions - Latest release: 7 months ago - 29.3 thousand downloads total - 1 maintainer
Top 6.9% on bioconductor.org
HTSFilter 1.42.0
Filter replicated high-throughput transcriptome sequencing data
3 versions - Latest release: 7 months ago - 1 dependent package - 41.6 thousand downloads total - 1 maintainer
Top 8.7% on bioconductor.org
genArise 1.78.0
Microarray Analysis tool
3 versions - Latest release: 7 months ago - 29.8 thousand downloads total - 1 maintainer
GPA 1.14.0
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
3 versions - Latest release: 7 months ago - 4.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
bigmelon 1.28.0
Illumina methylation array analysis for large experiments
3 versions - Latest release: 7 months ago - 12.3 thousand downloads total - 1 maintainer
netprioR 1.28.0
A model for network-based prioritisation of genes
3 versions - Latest release: 7 months ago - 9.03 thousand downloads total - 1 maintainer
qsmooth 1.18.0
Smooth quantile normalization
3 versions - Latest release: 7 months ago - 7.31 thousand downloads total - 1 maintainer
BUS 1.58.0
Gene network reconstruction
3 versions - Latest release: 7 months ago - 27.5 thousand downloads total - 1 maintainer
skewr 1.34.0
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
3 versions - Latest release: 7 months ago - 11.7 thousand downloads total - 1 maintainer
Spaniel 1.16.0
Spatial Transcriptomics Analysis
3 versions - Latest release: 7 months ago - 6.46 thousand downloads total - 1 maintainer
iBMQ 1.42.0
integrated Bayesian Modeling of eQTL data
3 versions - Latest release: 7 months ago - 16.8 thousand downloads total - 1 maintainer
flowCut 1.12.0
Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis
3 versions - Latest release: 7 months ago - 6.64 thousand downloads total - 1 maintainer
snm 1.50.0
Supervised Normalization of Microarrays
3 versions - Latest release: 7 months ago - 1 dependent package - 35.5 thousand downloads total - 1 maintainer
GOTHiC 1.38.0
Binomial test for Hi-C data analysis
3 versions - Latest release: 7 months ago - 22.2 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
nnNorm 2.66.0
Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
3 versions - Latest release: 7 months ago - 28.7 thousand downloads total - 1 maintainer
Related Keywords
Software 263 QualityControl 94 Microarray 90 ImmunoOncology 78 GeneExpression 78 Sequencing 74 Normalization 72 RNASeq 61 DataImport 61 Visualization 54 DifferentialExpression 51 TwoChannel 40 SingleCell 36 OneChannel 34 Transcriptomics 34 DNAMethylation 34 BatchEffect 31 Clustering 29 MultipleComparison 29 MassSpectrometry 23 Regression 23 Transcription 22 Proteomics 19 StatisticalMethod 19 Genetics 19 Coverage 19 Epigenetics 19 Alignment 18 Metabolomics 15 Classification 15 DataRepresentation 14 MethylationArray 14 CopyNumberVariation 13 FlowCytometry 13 FunctionalGenomics 13 GeneSetEnrichment 13 Bayesian 12 WorkflowStep 12 DifferentialMethylation 12 r 11 ChIPSeq 10 Annotation 10 CellBasedAssays 10 GeneRegulation 10 DimensionReduction 10 PrincipalComponent 10 TimeCourse 10 GUI 9 SNP 9 CpGIsland 9 bioconductor 8 mRNAMicroarray 8 SystemsBiology 8 GenomeAnnotation 8 BiomedicalInformatics 8 ExperimentalDesign 8 bioinformatics 8 AlternativeSplicing 7 Infrastructure 7 DifferentialSplicing 7 Network 7 CellBiology 6 ProprietaryPlatforms 6 ExonArray 6 Pathways 6 bioconductor-package 6 genomics 6 MultiChannel 5 ATACSeq 5 ReportWriting 5 single-cell 5 FeatureExtraction 5 PeakDetection 5 SequenceMatching 5 GraphAndNetwork 5 MethylSeq 4 GeneticVariability 4 rstats 4 Spatial 4 Cheminformatics 4 GenomeWideAssociation 4 ThirdPartyClient 4 r-package 4 MicroRNAArray 4 ChipOnChip 3 qPCR 3 DNASeq 3 DifferentialPeakCalling 3 Lipidomics 3 rna-seq 3 HiC 3 MicrotitrePlateAssay 2 GO 2 SangerSeq 2 ShinyApps 2 shiny 2 Survival 2 SupportVectorMachine 2 DecisionTree 2 pipeline 2