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Topic: SingleCell or SequencingData or Preprocessing

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Release: Release 3.8 (2018)

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348 packages on Bioconductor tagged SingleCell or SequencingData or Preprocessing, most distinct IPs first

SingleCell, SequencingData and Preprocessing in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
limma
Linear Models for Microarray and Omics DataGordon Smyth		Gordon Smythsoftware10 Aug 202645,9656
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202632,39210
SingleCellExperiment
S4 Classes for Single Cell DataDavide Risso		Davide Rissosoftware28 Apr 202624,48325
HDF5Array
HDF5 datasets as array-like objects in RHervé Pagès		Hervé Pagèssoftware28 Apr 202620,53728
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202612,63578
sva
Surrogate Variable AnalysisJeffrey T. Leek		Jeffrey T. Leeksoftware5 May 202610,80468
affy
Methods for Affymetrix Oligonucleotide ArraysRobert D. Shear		Robert D. Shearsoftware28 Apr 202610,55611
scran
Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202610,13962
vsn
Variance stabilization and calibration for microarray dataWolfgang Huber		Wolfgang Hubersoftware28 Apr 20267,53633
biovizBase
Basic graphic utilities for visualization of genomic data.Michael Lawrence		Michael Lawrencesoftware28 Apr 20266,487126
tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysisMichael Love		Michael Lovesoftware28 Apr 20265,8043
slingshot
Tools for ordering single-cell sequencingKelly Street		Kelly Streetsoftware28 Apr 20264,68438
AUCell
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)Gert Hulselmans		Gert Hulselmanssoftware29 Apr 20264,610115
DropletUtils
Utilities for Handling Single-Cell Droplet DataJonathan Griffiths		Jonathan Griffithssoftware27 Sep 20264,10759
oligo
Preprocessing tools for oligonucleotide arraysBenilton Carvalho		Benilton Carvalhosoftware28 Apr 20264,08752
minfi
Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 20264,041143
cytolib
C++ infrastructure for representing and interacting with the gated cytometry dataMike Jiang		Mike Jiangsoftware28 Apr 20263,8208
MAST
Model-based Analysis of Single Cell TranscriptomicsAndrew McDavid		Andrew McDavidsoftware28 Apr 20263,74056
HSMMSingleCell
Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)Cole Trapnell		Cole Trapnellexperiment5 May 20263,5530
marray
Exploratory analysis for two-color spotted microarray dataYee Hwa (Jean) Yang		Yee Hwa (Jean) Yangsoftware28 Apr 20263,3117
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20263,21199
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
airway
RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014Michael Love		Michael Loveexperiment5 May 20262,85425
methylumi
Handle Illumina methylation dataSean Davis		Sean Davissoftware16 Aug 20262,825158
flowWorkspace
Infrastructure for representing and interacting with gated and ungated cytometry data sets.Greg Finak		Greg Finaksoftware28 Apr 20262,80461
EDASeq
Exploratory Data Analysis and Normalization for RNA-SeqDavide Risso		Davide Rissosoftware28 Apr 20262,602111
tximeta
Transcript Quantification Import with Automatic MetadataMichael Love		Michael Lovesoftware26 Oct 20262,485108
aroma.light
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data TypesHenrik Bengtsson		Henrik Bengtssonsoftware28 Apr 20262,4818
lumi
BeadArray Specific Methods for Illumina Methylation and Expression MicroarraysLei Huang		Lei Huangsoftware28 Apr 20262,454165
affyPLM
Methods for fitting probe-level modelsBen Bolstad		Ben Bolstadsoftware28 Apr 20262,43022