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Topic: ChIPSeq or DataImport

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Release: Release 3.7 (2018)

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252 packages on Bioconductor tagged ChIPSeq or DataImport, most distinct IPs first

ChIPSeq and DataImport 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
DESeq2
Differential gene expression analysis based on the negative binomial distributionMichael Love		Michael Lovesoftware28 Apr 202632,07254
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
BiocFileCache
Manage Files Across SessionsLori Shepherd		Lori Shepherdsoftware28 Apr 202629,41641
Rhtslib
HTSlib high-throughput sequencing library as an R packageHervé Pagès		Hervé Pagèssoftware28 Apr 202628,0831
rhdf5
R Interface to HDF5Hugo Gruson		Hugo Grusonsoftware14 Sep 202627,6208
GenomicAlignments
Representation and manipulation of short genomic alignmentsHervé Pagès		Hervé Pagèssoftware28 Apr 202627,00641
rtracklayer
R interface to genome annotation files and the UCSC genome browserMichael Lawrence		Michael Lawrencesoftware28 Apr 202626,11956
SingleCellExperiment
S4 Classes for Single Cell DataDavide Risso		Davide Rissosoftware28 Apr 202624,48325
beachmat
Compiling Bioconductor to Handle Each Matrix TypeAaron Lun		Aaron Lunsoftware28 Apr 202622,12123
HDF5Array
HDF5 datasets as array-like objects in RHervé Pagès		Hervé Pagèssoftware28 Apr 202620,53728
GEOquery
Get data from NCBI Gene Expression Omnibus (GEO)Sean Davis		Sean Davissoftware25 Oct 202615,96073
AnnotationHub
Client to access AnnotationHub resourcesBioconductor Package Maintainer		Bioconductor Package Maintainersoftware2 Jul 202615,67262
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202612,63578
ExperimentHub
Client to access ExperimentHub resourcesBioconductor Package Maintainer		Bioconductor Package Maintainersoftware19 Aug 202611,14663
affyio
Tools for parsing Affymetrix data filesBen Bolstad		Ben Bolstadsoftware28 Apr 202610,6151
VariantAnnotation
Annotation of Genetic VariantsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20269,66476
ShortRead
FASTQ input and manipulationBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20268,12653
biomformat
An interface package for the BIOM file formatPaul J. McMurdie		Paul J. McMurdiesoftware28 Apr 20267,8379
tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysisMichael Love		Michael Lovesoftware28 Apr 20265,8043
mzR
parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)Steffen Neumann		Steffen Neumannsoftware28 Apr 20265,63915
MSnbase
Base Functions and Classes for Mass Spectrometry and ProteomicsLaurent Gatto		Laurent Gattosoftware9 Aug 20265,521134
DECIPHER
Tools for curating, analyzing, and manipulating biological sequencesErik Wright		Erik Wrightsoftware30 Jul 20264,88216
mzID
An mzIdentML parser for RLaurent Gatto		Laurent Gattosoftware28 Apr 20264,53211
monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqCole Trapnell		Cole Trapnellsoftware28 Apr 20264,48574
illuminaio
Parsing Illumina Microarray Output FilesKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 20264,4194