Our lab collaborates closely with the bioinformatics facility headed by Dr. Thomas Manke to help develop data analysis tools. Members of the Akhtar lab have contributed to multiple publicly available software packages, a selection of which is given below.
Set of programs to process, analyze and visualize Hi-C and cHi-C data
Hi-C scaffolding tool to assemble contigs/scaffolds into complete chromosomes
User-friendly tools for exploring deep-sequencing data
snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data
deepStats is a statistical and dataviz toolbox for deeptools, genomic signals, and more (GOterms, etc)
An R package for analysis of data produced by transcript 5' profiling methods like RAMPAGE and MAPCap