Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Papers: 10.1186/1471-2105-11-237

https://doi.org/10.1186/1471-2105-11-237

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

Cited by: 868
Author(s): Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon Lin, David S. Lapointe, Michael R. Green
Published: over 14 years ago

Software Mentions 16

bioconductor: ACME
Algorithms for Calculating Microarray Enrichment (ACME)
Papers that mentioned: 63
bioconductor: biomaRt
Interface to BioMart databases (i.e. Ensembl)
Papers that mentioned: 446
bioconductor: Biostrings
Efficient manipulation of biological strings
Papers that mentioned: 220
bioconductor: BSgenome
Software infrastructure for efficient representation of full genomes and their SNPs
Papers that mentioned: 47
bioconductor: ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
Papers that mentioned: 145
bioconductor: chipseq
chipseq: A package for analyzing chipseq data
Papers that mentioned: 9
bioconductor: ChIPseqR
Identifying Protein Binding Sites in High-Throughput Sequencing Data
Papers that mentioned: 5
bioconductor: DEGseq
Identify Differentially Expressed Genes from RNA-seq data
Papers that mentioned: 697
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
bioconductor: GenomicFeatures
Conveniently import and query gene models
Papers that mentioned: 141
bioconductor: IRanges
Foundation of integer range manipulation in Bioconductor
Papers that mentioned: 62
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: multtest
Resampling-based multiple hypothesis testing
Papers that mentioned: 158
bioconductor: Ringo
R Investigation of ChIP-chip Oligoarrays
Papers that mentioned: 36
bioconductor: rtracklayer
R interface to genome annotation files and the UCSC genome browser
Papers that mentioned: 107
bioconductor: ShortRead
FASTQ input and manipulation
Papers that mentioned: 119