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Topic: Epigenetics or Alignment

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Release: Release 3.17 (2023)

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188 packages on Bioconductor tagged Epigenetics or Alignment, most distinct IPs first

Epigenetics and Alignment 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
ggtree
an R package for visualization of tree and annotation dataGuangchuang Yu		Guangchuang Yusoftware29 Oct 202634,37279
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202632,39210
treeio
Base Classes and Functions for Phylogenetic Tree Input and OutputGuangchuang Yu		Guangchuang Yusoftware30 Apr 202631,96639
Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202630,33728
GenomicAlignments
Representation and manipulation of short genomic alignmentsHervé Pagès		Hervé Pagèssoftware28 Apr 202627,00641
DECIPHER
Tools for curating, analyzing, and manipulating biological sequencesErik Wright		Erik Wrightsoftware30 Jul 20264,88216
TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) AnalysisGe Tan		Ge Tansoftware28 Apr 20264,72179
bumphunter
Bump HunterTamilselvi Guharaj		Tamilselvi Guharajsoftware28 Apr 20264,26883
minfi
Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 20264,041143
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20263,21199
msa
Multiple Sequence AlignmentUlrich Bodenhofer		Ulrich Bodenhofersoftware12 Aug 20262,97216
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
systemPipeR
systemPipeR: A Multipurpose Workflow Management System for Reproducible Data AnalysisThomas Girke		Thomas Girkesoftware28 Apr 20262,50694
DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataRory Stark		Rory Starksoftware21 Jul 20262,490141
bamsignals
Extract read count signals from bam filesJohannes Helmuth		Johannes Helmuthsoftware21 May 20262,20214
GreyListChIP
Grey Lists -- Mask Artefact Regions Based on ChIP InputsMatt Eldridge		Matt Eldridgesoftware28 Apr 20261,94259
DMRcate
Methylation array and sequencing spatial analysis methodsTim Peters		Tim Peterssoftware3 May 20261,838224
EpiDISH
Epigenetic Dissection of Intra-Sample-HeterogeneityShijie C. Zheng		Shijie C. Zhengsoftware28 Apr 20261,79363
motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequenceJianhong Ou		Jianhong Ousoftware28 Apr 20261,782111
QuasR
Quantify and Annotate Short Reads in RMichael Stadler		Michael Stadlersoftware28 Apr 20261,551114
TOAST
Tools for the analysis of heterogeneous tissuesZiyi Li		Ziyi Lisoftware28 Apr 20261,454102
R4RNA
An R package for RNA visualization and analysisDaniel Lai		Daniel Laisoftware28 Apr 20261,35215
RnBeads
RnBeadsFabian Mueller		Fabian Muellersoftware28 Apr 20261,302170
ggmsa
Plot Multiple Sequence Alignment using 'ggplot2'Guangchuang Yu		Guangchuang Yusoftware28 Apr 20261,23193
singleCellTK
Comprehensive and Interactive Analysis of Single Cell RNA-Seq DataJoshua David Campbell		Joshua David Campbellsoftware29 Apr 20261,218392
Rbowtie
R bowtie wrapperMichael Stadler		Michael Stadlersoftware28 Apr 20261,2111
dmrseq
Detection and inference of differentially methylated regions from Whole Genome Bisulfite SequencingKeegan Korthauer		Keegan Korthauersoftware28 Apr 20261,201149
amplican
Automated analysis of CRISPR experimentsEivind Valen		Eivind Valensoftware28 Apr 20261,200102