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Topic: SingleCell or Alignment or Preprocessing

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Release: Release 2.12 (2013)

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115 packages on Bioconductor tagged SingleCell or Alignment or Preprocessing, most distinct IPs first

SingleCell, Alignment and Preprocessing in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
Biostrings
Efficient manipulation of biological stringsHervé Pagès		Hervé Pagèssoftware2 Sep 202658,96214
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
Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202630,33728
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
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
DECIPHER
Tools for curating, analyzing, and manipulating biological sequencesErik Wright		Erik Wrightsoftware30 Jul 20264,88216
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
marray
Exploratory analysis for two-color spotted microarray dataYee Hwa (Jean) Yang		Yee Hwa (Jean) Yangsoftware28 Apr 20263,3117
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
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
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
Mfuzz
Soft clustering of omics time series dataMatthias Futschik		Matthias Futschiksoftware28 Apr 20262,35316
gcrma
Background Adjustment Using Sequence InformationZ. Wu		Z. Wusoftware28 Apr 20262,28521
motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequenceJianhong Ou		Jianhong Ousoftware28 Apr 20261,782111
beadarray
Quality assessment and low-level analysis for Illumina BeadArray dataMark Dunning		Mark Dunningsoftware31 Aug 20261,74065
wateRmelon
Illumina DNA methylation array normalization and metricsLeo C Schalkwyk		Leo C Schalkwyksoftware28 Apr 20261,720172
QuasR
Quantify and Annotate Short Reads in RMichael Stadler		Michael Stadlersoftware28 Apr 20261,551114
piano
Platform for integrative analysis of omics dataLeif Varemo Wigge		Leif Varemo Wiggesoftware28 Apr 20261,50994
crlmm
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arraysBenilton S Carvalho		Benilton S Carvalhosoftware28 Apr 20261,50465
affycomp
Graphics Toolbox for Assessment of Affymetrix Expression MeasuresRobert D. Shear		Robert D. Shearsoftware28 Apr 20261,3397
makecdfenv
CDF Environment MakerJames W. MacDonald		James W. MacDonaldsoftware28 Apr 20261,32012
puma
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)Xuejun Liu		Xuejun Liusoftware28 Apr 20261,29655