Home

Welcome to the Bioinformatics-scripts wiki! Let's explain all the repositories.

1. Repository: /ySGD_converter

A converter from Saccharomyces Genome Database (SGD) ID to Gene name and vice versa.

• Option 1: Convert SGDID to Gene name
• Option 2: Convert Gene name to SGDID
• Examples in usage.py

2. Script: topGO.R

R script to execute a gene set enrichment analysis

3. Script: Manipulação de vias KEGG em python

Manipulating KEGG pathways using Python. Including search for genes in any pathway, reactions, maps and more. I leave you a script. Manipulation performed by two packages: Biopython and Bioservices.

4. Script: DESeq2.R

R script for differential expression analysis using DESeq2

5. Script: NetworkX analysis

Python script for networkX analysis using STRING database

6. Script: WGCNA analysis

R script for WGCNA analysis, including module detection, network construction and traits association

Python script for networkX analysis using STRING database

7. Script: Finding gaps and indels of best HSP (lowest e-value) in blast XML file

A script that takes the .XML files generated when someone performs a BlastP against our dataset and prints as output a text file containing the position of the gaps and indels that were found in the alignment, with the position of these mutations and what was the replacement of amino acids preferably in the A123B format, where "A" is the amino acid in the reference sequence, "123" is the position in the alignment, and "B" is the amino acid in the query sequence.

Another script reports all gaps and indels in all HSP, not only in the best. It's found here.