Intro
Queries the DAVID database for an enrichment analysis and plots CellPlots as well as SymPlots (see plots).
Examples
$ cat input.tsv
ensembl_gene_id log2(fold_change)
ENSG00000272449 1.859500
ENSG00000130762 0.601051
ENSG00000083444 -0.881957
ENSG00000162493 -0.638433
ENSG00000253368 0.654517
$ david -i input.tsv -o /usr/home/JDoe/project1/datasetA -d ENSEMBL_GENE_ID -u 'email.registered@david.com'
Help
$ david --help
usage: david [-h] [-i INPUT] [-o OUTPUT] [-d DATABASE] [-c CATEGORIES]
[-u USER] [-v] [-p PVALUE] [-n NGENES] [-b BACKGROUND]
Queries the DAVID database for an enrichment analysis and plots CellPlots as
well as SymPlots (see plots). Check
https://david.ncifcrf.gov/content.jsp?file=DAVID_API.html for database ==
'type' tag and categories == 'annot' tag.
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
A file with tab separated values where the first
column contains the identifiers to be queried and the
second column the respective log2fc for each
identifier. (default: None)
-o OUTPUT, --output OUTPUT
/path/to/output/prefix (default: None)
-d DATABASE, --database DATABASE
a string for the database to query, e.g.
'WORMBASE_GENE_ID'. (default: None)
-c CATEGORIES, --categories CATEGORIES
a comma separated list of categories. (default: GOTERM
_BP_FAT,GOTERM_CC_FAT,GOTERM_MF_FAT,KEGG_PATHWAY,BIOCA
RTA,PFAM,PROSITE)
-u USER, --user USER a user ID registered at DAVID for querying (default:
None)
-v, --verbose Print more. (default: None)
-p PVALUE, --pvalue PVALUE
Maximum p value for enrichment of a term. (default:
0.1)
-n NGENES, --ngenes NGENES
Minimum number of genes within a term. (default: 2)
-b BACKGROUND, --background BACKGROUND
A file with tab separated values where the first
column contains the identifiers to used as a
background. None for whole DAVID database as
background. (default: None)