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genescf_README.txt
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genescf_README.txt
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Gene Set Clustering based on Functional annotation
----------------------------------------------------------------------------
Hosting website: https://genescf.kandurilab.org
INSTALL:
No installation of GeneSCF required. The plot function in GeneSCF needs 'ggplot2' R package (R version > 3.0).
GeneSCF USAGE:
./geneSCF -m=[update|normal] -i=[INPUT_PATH/INPUT_FILE] -t=[gid|sym] -o=[OUTPUT_PATH/FOLDER/] -db=[GO_all|GO_BP|GO_MF|GO_CC|KEGG|REACTOME|NCG] -p=[yes|no] -bg=[#TotalGenes] -org=[see,org_codes_help]
==========
Options: ALL PARAMETERS MUST BE SPECIFIED
==========
[-m= | --mode=] For normal mode use 'normal' and for update mode use 'update' without quotes.
[-i= | --infile=] Input file contains list of Entrez GeneIDs or OFFICIAL GENE SYMBOLS.
The genes must be new lines seperated (One gene per line).
[-t= | --gtype=] Type of input in the provided list either Entrez GeneIDs 'gid'
or OFFICIAL GENE SYMBOLS 'sym' (Without quotes, Example for
human 'sym' => HUGO gene symbols).
[-db= | --database=] Database to find gene enrichment which is either
geneontology 'GO_all' or geneontology-biological_process
'GO_BP' or geneontology-molecular_function 'GO_MF' or
geneontology-cellular_components 'GO_CC' or kegg 'KEGG' or
reactome 'REACTOME' or Network of Cancer Genes 'NCG' (Without quotes).
[-o= | --outpath=] Existing directory to save output file. The output will be with saved in the
provided location as {INPUT_FILE_NAME}_{database}_functional_classification.tsv
(tab-seperated file).
[-bg= | --background=] Total background genes to consider (Example : ~20,000 for human).
[-org= | --organism=] Please see organism codes(For human in KEGG ->'hsa' in Geneontology -> 'goa_human').
For REACTOME and NCG use 'Hs' (human).
[-p= | --plot=] For additional graphical output use 'yes' or 'no'.This requires R version > 3.0 and
'ggplot2' R package to be pre-installed on the system.
[-h | --help] For displaying this help page.
prepare_database USAGE:
./prepare_database -db=[GO_all|GO_BP|GO_MF|GO_CC|KEGG|REACTOME|NCG] -org=[see,org_codes_help]
==========
Options: ALL PARAMETERS MUST BE SPECIFIED
==========
[-db= | --database=] Options:[GO_all|GO_BP|GO_MF|GO_CC|KEGG|REACTOME]
[-org= | --organism=] Options:[see,org_codes_help]
--------------------------
Cite using:
Subhash, S. & Kanduri, C. GeneSCF: a real-time based functional enrichment tool with support
for multiple organisms. BMC Bioinformatics 17, 365 (2016). [doi:10.1186/s12859-016-1250-z] [PMC5020511]
--------------------------
Author: Santhilal Subhash
Last Updated: 2017/01/13
https://genescf.kandurilab.org