abearab

Incoming PhD candidate @UCSF • Genetics, Functional Genomics, Systems & Synthetic Biology

UCSFEarth

Pinned Repositories

abearab
0 1 10
abolfazlarab
Language:HTML0 1 00
imRIP
Integrated methods for meRIP-seq data analysis
Language:Shell1 1 51
QuantSeq-FWD-with-UMIs
QuantSeq FWD with UMIs RNA-seq analysis pipeline
Language:R1 1 01
skywalkR-graph-features
Example notebooks that illustrate how to generate knowledge-based features. Features can be used in a variety of ML models, including recommender systems.
Language:Jupyter Notebook10
ScreenPro2
Flexible analysis of high-content CRISPR screening
Language:Python10 1 431
CanDI
CanDI - A global cancer data integrator
Language:Jupyter Notebook6 4 215
Decitabine-treatment
A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation
Language:Jupyter Notebook10
PrimeKG
Precision Medicine Knowledge Graph (PrimeKG)
Language:Jupyter Notebook346 11 1778
TDC
Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science
Language:Jupyter Notebook950 27 112169

abearab's Repositories

abearab/abearab
0 1 10
abearab/abolfazlarab
Language:HTML0 1 00
abearab/adpbulk
pseudobulking on an AnnData object
Language:Python0 0 00
abearab/CanDI
CanDI - A global cancer data integrator
Language:Jupyter Notebook0 0 00
abearab/CRISPRi-dual-sgRNA-screens
Language:Python0 0 00
abearab/pager
PAGE algorithm run and downstream analysis
Language:Jupyter Notebook0 1 50
abearab/psix
A computational tool for identifying cell-state associated alternative splicing events in scRNA-seq
Language:Python00
abearab/PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Language:Python0 0 00
abearab/sc-haircut-net
Network analysis pipeline for simultaneous measurement of DNA repair activities and mRNA abundance in single cells
Language:eC00
abearab/awesome-CRISPR
List of software/websites/databases/other stuff for genome engineering
0 0
abearab/biobear
Work with bioinformatic files using Arrow, Polars, and/or DuckDB
Language:Rust
abearab/Cancer-Cell-Encoder
Language:Jupyter Notebook1 1
abearab/casmap
Mapping sgRNA counts for cas12 6-mer CRISPR screens
Language:Rust0 0
abearab/celligner
tumor - cancer cell line alignment. Use it on the depmap portal or install it with pip.
abearab/CRISPR-screening-vocabulary
1 0
abearab/easyDataverse
🪐 - Lightweight Dataverse interface in Python to upload, download and update datasets found in Dataverse installations.
abearab/gget
🧬 gget enables efficient querying of genomic reference databases
Language:Python
abearab/GISEA
Genetic Interaction Networks and Pathway Modules
Language:Python1 3
abearab/herken2022_originalcode
original code for the manuscript "Environmental challenge rewires functional connections among human genes"
Language:Jupyter Notebook
abearab/HERVs
Human endogenous retroviruses (HERV)
Language:Jupyter Notebook
abearab/learn-rust
Language:Rust
abearab/PosSpacer
A framework for preprocessing multiplexed CRISPR libraries
Language:Python
abearab/PrimeKG
Precision Medicine Knowledge Graph (PrimeKG)
Language:Jupyter Notebook
abearab/pvsvg
a python wrapper of the vis.js network visualization library with an additional ability to export static SVG
Language:JavaScript
abearab/pypage
python implementation of the PAGE algorithm
Language:Python0 0
abearab/REMBRANDTS
REMoving Bias from Rna-seq ANalysis of Differential Transcript Stability
Language:R0 0
abearab/RNAtargeting_web_custom
source code of the custom page for the RNA targeting website - Cas13d guide design
abearab/single-cell-vocabulary
0 0
abearab/SwitchFinder
abearab/TDC
Therapeutics Data Commons: Artificial Intelligence Foundation for Therapeutic Science
Language:Jupyter Notebook