| This workflow extracts genetic information from this microarray data, and finds relationships between cis-regulatory elements located in the promoter under same regulation of gene expression. |
hg clone https://toolshed.g2.bx.psu.edu/repos/amadeo/amadeo
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| tool to compare contigous motifs in gff file and, in case that two overlap, remove the motif with the highest p value | 1.0.0 | any | |
| Script that takes a gff format file from MEME suite as input and orders it by genes, so it will create an output with all the information grouped by genes. Motifs will be mixed. | 1.0.0 | any | |
| Script that takes a gff format file from step1.pl as input and orders each block of gene data by the start position of the motif. | 1.0.0 | any | |
| tool prints out motifs of a certain rule that are present in a gene | 1.0.0 | any | |
| tool that looks for genes that have motifs from a certain rule | 1.0.0 | any | |
| Script that takes a gff format file from step1.pl as input and orders each block of gene data by the start position of the motif. | 1.0.0 | any | |
| Script that takes a gff format file from MEME suite as input and orders it by genes, so it will create an output with all the information grouped by genes. Motifs will be mixed. | 1.0.0 | any | |
| Script to compare contigous motifs in gff file and, in case that two overlap, remove the motif with the highest p value | 1.0.0 | any | |
| Script to create csv formatted gene vs TF matrix from a filtered gff file. GFF file can contain just Positive or Just neagtive strand TFBS. Has two types of matrix produced: (0) resence/Abscence with only 1 and 0s. With option=0. (1) counts of TFs with numbers 1,3,5 etc. | 1.0.0 | any | |
| re-writes a fasta file with compatible headers for MEME suite tool. | 1.0.0 | any | |
| Script to take a list of JASPAR ids and extract a subset of matrix information for each of them from a meme file | 1.0.0 | any | |
| Script to take output from AME (part of memesuite-org) and extract a list of the overrepresented motifs | 1.0.0 | any | |
| Extract the motifs names from ame processed file | 1.0.0 | any | |
| Script to take sort block of genes in a .gff file by the start position of the motifs | 1.0.0 | any | |
| Script to compare same contigous motifs in gff file and, in case that two overlap, remove the motif with the highest p value | 1.0.0 | any | |