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: 10.1371/journal.pcbi.1000227

https://doi.org/10.1371/journal.pcbi.1000227

Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Published: over 15 years ago

Software Mentions 39

bioconductor: ACME
Algorithms for Calculating Microarray Enrichment (ACME)
Papers that mentioned: 63
bioconductor: affy
Methods for Affymetrix Oligonucleotide Arrays
Papers that mentioned: 989
bioconductor: affyio
Tools for parsing Affymetrix data files
Papers that mentioned: 5
bioconductor: annotate
Annotation for microarrays
Papers that mentioned: 36
bioconductor: AnnotationDbi
Manipulation of SQLite-based annotations in Bioconductor
Papers that mentioned: 73
bioconductor: arrayQualityMetrics
Quality metrics report for microarray data sets
Papers that mentioned: 190
bioconductor: Biobase
Biobase: Base functions for Bioconductor
Papers that mentioned: 104
bioconductor: biomaRt
Interface to BioMart databases (i.e. Ensembl)
Papers that mentioned: 446
bioconductor: genefilter
genefilter: methods for filtering genes from high-throughput experiments
Papers that mentioned: 142
bioconductor: geneplotter
Graphics related functions for Bioconductor
Papers that mentioned: 14
bioconductor: graph
graph: A package to handle graph data structures
Papers that mentioned: 45
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: oligo
Preprocessing tools for oligonucleotide arrays
Papers that mentioned: 204
bioconductor: preprocessCore
A collection of pre-processing functions
Papers that mentioned: 146
bioconductor: Ringo
R Investigation of ChIP-chip Oligoarrays
Papers that mentioned: 36
bioconductor: tilingArray
Transcript mapping with high-density oligonucleotide tiling arrays
Papers that mentioned: 17
bioconductor: topGO
Enrichment Analysis for Gene Ontology
Papers that mentioned: 652
bioconductor: vsn
Variance stabilization and calibration for microarray data
Papers that mentioned: 91
bioconductor: weaver
Tools and extensions for processing Sweave documents
Papers that mentioned: 1
cran: codetools
Code Analysis Tools for R
Papers that mentioned: 3
cran: digest
Create Compact Hash Digests of R Objects
Papers that mentioned: 10
cran: fortunes
R Fortunes
Papers that mentioned: 1
cran: KernSmooth
Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Papers that mentioned: 34
cran: lattice
Trellis Graphics for R
Papers that mentioned: 251
cran: RColorBrewer
ColorBrewer Palettes
Papers that mentioned: 490
cran: RCurl
General Network (HTTP/FTP/...) Client Interface for R
Papers that mentioned: 36
cran: RSQLite
SQLite Interface for R
Papers that mentioned: 27
cran: SparseM
Sparse Linear Algebra
Papers that mentioned: 7
cran: survival
Survival Analysis
Papers that mentioned: 1,690
cran: xtable
Export Tables to LaTeX or HTML
Papers that mentioned: 32
pypi: annotate
Decorator to set a function's __annotations__ like Py3.
Papers that mentioned: 36
pypi: codetools
code analysis and execution tools
Papers that mentioned: 3
pypi: digest
Calculate message digests of files or standard input
Papers that mentioned: 10
pypi: graph
Directed and undirected graph data structures and algorithms.
Papers that mentioned: 45
pypi: lattice
A framework for developing data models, including schema development and documentation.
Papers that mentioned: 251
pypi: oligo
UNOFFICIAL Python client for i-DE
Papers that mentioned: 204
pypi: survival
Add static script_dir() method to Path
Papers that mentioned: 1,690
pypi: weaver
Wrapper for Fabric
Papers that mentioned: 1
pypi: xtable
operate table format in console. console table, csv, json, yaml and markdown.
Papers that mentioned: 32