Pathview pipeline

Pathview specifications

Information


Unique identifier OMICS_05212
Name Pathview
Alternative name Pathview Web
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Weijun Luo <>

Additional information


https://pathview.uncc.edu/

Information


Unique identifier OMICS_05212
Name Pathview
Alternative name Pathview Web
Interface Web user interface
Restrictions to use None
Input data Some (1) gene data cover any data that map to unique gene IDs including genes, transcripts, genomic loci, proteins, enzymes and their attributes; (2) compound data cover any data that map to unique compound IDs including compounds, metabolites, drugs, small molecules and their attributes.
Output data Graphs with user data mapped.
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Weijun Luo <>

Additional information


https://pathview.uncc.edu/

Publications for Pathview

Pathview citations

 (2)
2018
PMCID: 5864062

[…] 0.05) contained in the tool., kegg metabolic maps for the enriched pathways were highlighted using fold change from normalized expression levels by transcripts per million (tpm) with the r package “pathview” [29] to compare expression levels in leaf and internode between koshu and pinot noir., first-strand cdna was synthesized from total rna with a primescript rt reagent kit with gdna eraser […]

2017
PMCID: 5339665

[…] analysis based on kegg pathway database (http://www.genome.jp/kegg/) was done using the r package gage v2.22 (luo et al., 2009). pathway-level differential expression was visually checked using pathview (luo and brouwer, 2013). functional classification of gene products was predicted using blastp v2.5.0+ (altschul et al., 1997) by the clusters within the orthologous group (cog) database […]

Pathview institution(s)
Department of Bioinformatics and Genomics, UNC Charlotte, Charlotte, NC, USA; UNC Charlotte Bioinformatics Service Division, North Carolina Research Campus, Kannapolis, NC, USA; Department of Computer Science, UNC Charlotte, Charlotte, NC, USA
Pathview funding source(s)
Supported by National Science Foundation [ABI-1565030]; UNC Charlotte CCI Faculty Innovation Award.

Pathview review

star_border star_border star_border star_border star_border
star star star star star

Martin Abba

star_border star_border star_border star_border star_border
star star star star star
Desktop
Nice R/Bioconductor package to visualize Differentially expressed genes and differentially methylated regions among KEGG based pathways just providing a gene Entrez ID list with their associated fold changes.