Abolfazl (Abe)'s repositories
adpbulk
pseudobulking on an AnnData object
CanDI
CanDI - A global cancer data integrator
psix
A computational tool for identifying cell-state associated alternative splicing events in scRNA-seq
PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
sc-haircut-net
Network analysis pipeline for simultaneous measurement of DNA repair activities and mRNA abundance in single cells
awesome-CRISPR
List of software/websites/databases/other stuff for genome engineering
biobear
Work with bioinformatic files using Arrow, Polars, and/or DuckDB
cancer_data
A unified downloader+preprocessor for cancer genomics datasets
casmap
Mapping sgRNA counts for cas12 6-mer CRISPR screens
celligner
tumor - cancer cell line alignment. Use it on the depmap portal or install it with pip.
easyDataverse
🪐 - Lightweight Dataverse interface in Python to upload, download and update datasets found in Dataverse installations.
gget
🧬 gget enables efficient querying of genomic reference databases
herken2022_originalcode
original code for the manuscript "Environmental challenge rewires functional connections among human genes"
HERVs
Human endogenous retroviruses (HERV)
PosSpacer
A framework for preprocessing multiplexed CRISPR libraries
PrimeKG
Precision Medicine Knowledge Graph (PrimeKG)
pvsvg
a python wrapper of the vis.js network visualization library with an additional ability to export static SVG
pypage
python implementation of the PAGE algorithm
REMBRANDTS
REMoving Bias from Rna-seq ANalysis of Differential Transcript Stability
RNAtargeting_web_custom
source code of the custom page for the RNA targeting website - Cas13d guide design
TDC
Therapeutics Data Commons: Artificial Intelligence Foundation for Therapeutic Science