abearab

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

UCSFEarth

Pinned Repositories

BMI-206-Class-Project
SCENT (Tissue-specific enhancer-gene) | BMI-206 Class Project
Language:Jupyter Notebook1 0 40
imRIP
Integrated methods for meRIP-seq data analysis
Language:Shell1 1 51
MultiOmics
A multi-omics analytic framework to study RNA dynamics
Language:Python00
pager
PAGE algorithm run and downstream analysis
Language:Jupyter Notebook0 1 100
PrimeKG
Precision Medicine Knowledge Graph (PrimeKG)
Language:Jupyter Notebook1 0 00
QuantSeq-FWD-with-UMIs
QuantSeq FWD with UMIs RNA-seq analysis pipeline
Language:R1 1 01
scez
Single Cell Analysis, Easy Mode!
Language:Python0 2 180
ScreenPro2
Flexible analysis of high-content CRISPR screening
Language:Python21 1 604
CanDI
CanDI - A global cancer data integrator
Language:Jupyter Notebook6 4 234
TDC
Therapeutics Commons (TDC-2): Multimodal Foundation for Therapeutic Science
Language:Jupyter Notebook1k 26 136177

abearab's Repositories

abearab/BMI-206-Class-Project
SCENT (Tissue-specific enhancer-gene) | BMI-206 Class Project
Language:Jupyter Notebook1 0 40
abearab/PrimeKG
Precision Medicine Knowledge Graph (PrimeKG)
Language:Jupyter Notebook1 0 00
abearab/abearab
0 1 10
abearab/abolfazlarab
Language:HTML0 1 00
abearab/CRISPRi-dual-sgRNA-screens
Language:Python0 0 00
abearab/pager
PAGE algorithm run and downstream analysis
Language:Jupyter Notebook0 1 100
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:Jupyter Notebook0 1 01
abearab/scez
Single Cell Analysis, Easy Mode!
Language:Python0 2 180
abearab/awesome-CRISPR
List of software/websites/databases/other stuff for genome engineering
0 0
abearab/blitzgsea
Fast Gene Set Enrichment Analysis (GSEA) implementation of the prerank algorithm. Use Loess interpolation of bimodal ES distribution for accurate p-value estimation.
Language:Jupyter Notebook0 0
abearab/bmi206-course
Language:HTML1 0
abearab/Cancer-Cell-Encoder
Language:Jupyter Notebook1 1
abearab/cancer_data
A unified downloader+preprocessor for cancer genomics datasets
Language:Python0 0
abearab/celligner
tumor - cancer cell line alignment. Use it on the depmap portal or install it with pip.
Language:Jupyter Notebook0 0
abearab/DeepGSEA
Language:Python0 0
abearab/enformer_fine_tuning
For fine-tuning Enformer using paired WGS & gene expression data
Language:Python0 0
abearab/gget
🧬 gget enables efficient querying of genomic reference databases
Language:Python0 0
abearab/herken2022_originalcode
original code for the manuscript "Environmental challenge rewires functional connections among human genes"
Language:Jupyter Notebook0 0
abearab/HERVs
Human endogenous retroviruses (HERV)
Language:Jupyter Notebook1 3
abearab/learn-rust
Language:Rust1 0
abearab/ml-pitfalls
Notebooks accompanying the paper "Navigating the pitfalls of applying machine learning in genomics"
Language:Jupyter Notebook0 0
abearab/omicverse
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
abearab/PosSpacer
A framework for preprocessing multiplexed CRISPR libraries
Language:Python2 4
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/single-cell-vocabulary
0 0
abearab/SuPreMo
Pipeline for generating reference and perturbed sequences for input into predictive models.
Language:Jupyter Notebook0 0
abearab/TDC
Therapeutics Data Commons: Artificial Intelligence Foundation for Therapeutic Science
Language:Jupyter Notebook0 0