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Topic: SingleCell or Alignment or DNAMethylation

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Release: Release 2.12 (2013)

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37 packages on Bioconductor tagged SingleCell or Alignment or DNAMethylation, most distinct IPs first

SingleCell, Alignment and DNAMethylation in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
Biostrings
Efficient manipulation of biological stringsHervé Pagès		Hervé Pagèssoftware2 Sep 202658,96214
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
DECIPHER
Tools for curating, analyzing, and manipulating biological sequencesErik Wright		Erik Wrightsoftware30 Jul 20264,88216
bumphunter
Bump HunterTamilselvi Guharaj		Tamilselvi Guharajsoftware28 Apr 20264,26883
minfi
Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 20264,041143
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
bsseq
Analyze, manage and store whole-genome methylation dataKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 20262,71889
lumi
BeadArray Specific Methods for Illumina Methylation and Expression MicroarraysLei Huang		Lei Huangsoftware28 Apr 20262,454165
motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequenceJianhong Ou		Jianhong Ousoftware28 Apr 20261,782111
IlluminaHumanMethylation450kmanifest
Annotation for Illumina's 450k methylation arraysKasper Daniel Hansen		Kasper Daniel Hansenannotationno date on record1,773144
wateRmelon
Illumina DNA methylation array normalization and metricsLeo C Schalkwyk		Leo C Schalkwyksoftware28 Apr 20261,720172
DSS
Dispersion shrinkage for sequencing dataHao Wu		Hao Wusoftware28 Apr 20261,70291
QuasR
Quantify and Annotate Short Reads in RMichael Stadler		Michael Stadlersoftware28 Apr 20261,551114
FDb.InfiniumMethylation.hg19
Annotation package for Illumina Infinium DNA methylation probesTim Triche, Jr.		Tim Triche, Jr.annotationno date on record1,48377
IlluminaHumanMethylationEPICmanifest
Manifest for Illumina's EPIC methylation arraysKasper Daniel Hansen		Kasper Daniel Hansenannotationno date on record1,449144
Rbowtie
R bowtie wrapperMichael Stadler		Michael Stadlersoftware28 Apr 20261,2111
segmentSeq
Methods for identifying small RNA loci from high-throughput sequencing dataSamuel Granjeaud		Samuel Granjeaudsoftware28 Apr 20261,17059
MethylSeekR
Segmentation of Bis-seq dataLukas Burger		Lukas Burgersoftware28 Apr 20261,09383
MEDIPS
DNA IP-seq data analysisLukas Chavez		Lukas Chavezsoftware28 Apr 20261,093102
BiSeq
Processing and analyzing bisulfite sequencing dataKatja Hebestreit		Katja Hebestreitsoftware28 Apr 20261,05189
TurboNorm
A fast scatterplot smoother suitable for microarray normalizationMaarten van Iterson		Maarten van Itersonsoftware28 Apr 20261,00618
HELP
Tools for HELP data analysisReid F. Thompson		Reid F. Thompsonsoftware28 Apr 20269328
MEDME
Modelling Experimental Data from MeDIP EnrichmentMattia Pelizzola		Mattia Pelizzolasoftware28 Apr 202688993
les
Identifying Differential Effects in Tiling Microarray DataJulian Gehring		Julian Gehringsoftware28 Apr 202688113
Repitools
Epigenomic tools		no date on record818
TransView
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets		no date on record732
ARRmNormalization
Adaptive Robust Regression normalization for Illumina methylation dataJean-Philippe Fortin		Jean-Philippe Fortinsoftware28 Apr 20267131
gmapR
An R interface to the GMAP/GSNAP/GSTRUCT suiteMichael Lawrence		Michael Lawrencesoftware28 Apr 202671377