Sergio Emilio Mares's repositories
atac-seq-pipeline
ENCODE ATAC-seq pipeline
BE131
UC Berkeley 2018 Fall BIOENG 131 : Introduction to Computational Molecular and Cellular Biology
carP-encoding-a-Ca2--regulated-putative-phytase
Here, we studied the conservation of carP sequence and its occurrence in diverse phylogenetic groups of bacteria. In silico analysis revealed that carP and its two paralogues PA2017 and PA0319 are primarily present in P. aeruginosa and belong to the core genome of the species.
diffhash
Find regions of differential expression by looking at kmer counts.
MAP-Pseudomonas-calC
Calcium leak channel (CalC) regulatory role in Pseudomonas aeruginosa virulence and interactions with the host.
megaprobe-lab
Sources for the MegaProbe lab web pages.
Pseudomonas-database-species-counter
Using Pseudomonas.com (blastN or blastP) searches, this code will pull out the species found in the input csv file and make a count for each species, useful for graphics.
PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.