mubashermohammed Goto Github PK

alona

analysis of single cell RNA sequencing data and cell type annotation

autodock-vina

AutoDock Vina

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

awesome_bigdata_ai_drugdiscovery

A collection of resources useful for leveraging big data and AI for drug discovery. It mainly serves as an orientation for new lab folks. It may be biased towards my lab interest.

balsamic

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

besca

BESCA (BEDA’s single cell sequencing analysis) offers python functions for single-cell analysis

cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

cellrank

CellRank for directed single-cell fate mapping

clusterprofiler

:bar_chart: A universal enrichment tool for interpreting omics data

cut-runtools-2.0

cytopath

Simulation based inference of differentiation trajectories from RNA velocity fields.

deep_learning_notes

deepscreen

DEEPScreen: Virtual Screening with Deep Convolutional Neural Networks Using Compound Images

deeptools

Tools to process and analyze deep sequencing data.

dltk

Deep Learning Toolkit for Medical Image Analysis

drugex

De Novo Design of Drug Molecule by Pareto-based Multi-Objective Reinforcement Learning in Polypharmacology

emap2secplus

Emap2sec+: Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning

episcanpy

Episcanpy: Epigenomics Single Cell Analysis in Python

flair

Full-Length Alternative Isoform analysis of RNA

gastrulation_analysis

gatk

Official code repository for GATK versions 4 and up

geneticalgorithmpython

Source code of PyGAD, a Python 3 library for building the genetic algorithm and training machine learning algorithms (Keras & PyTorch).

genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)

gfpgan

GFPGAN aims at developing Practical Algorithms for Real-world Face Restoration.

gnn_dove

Code for "Protein Docking Model Evaluation by Graph Neural Networks"

ibm3202

Google Colab Tutorials for IBM3202

idp_lzerd

Modeling disordered protein interactions from biophysical principles

imagelearning

exploratory image learning study

infercnv

Inferring CNV from Single-Cell RNA-Seq

jupyter_dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.