Pinned Repositories
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
Mosq_hemocytes
Single-cell-P.falciparum-midgut
analysis script
MubasherMohammed's Repositories
MubasherMohammed/Mosq_hemocytes
MubasherMohammed/BALSAMIC
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
MubasherMohammed/besca
BESCA (BEDA’s single cell sequencing analysis) offers python functions for single-cell analysis
MubasherMohammed/cell2location
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
MubasherMohammed/cellrank
CellRank for directed single-cell fate mapping
MubasherMohammed/Single-cell-P.falciparum-midgut
analysis script
MubasherMohammed/CUT-RUNTools-2.0
MubasherMohammed/deep_learning_notes
MubasherMohammed/epiScanpy
Episcanpy: Epigenomics Single Cell Analysis in Python
MubasherMohammed/flair
Full-Length Alternative Isoform analysis of RNA
MubasherMohammed/gatk
Official code repository for GATK versions 4 and up
MubasherMohammed/GeneticAlgorithmPython
Source code of PyGAD, a Python 3 library for building the genetic algorithm and training machine learning algorithms (Keras & PyTorch).
MubasherMohammed/GFPGAN
GFPGAN aims at developing Practical Algorithms for Real-world Face Restoration.
MubasherMohammed/ibm3202
Google Colab Tutorials for IBM3202
MubasherMohammed/infercnv
Inferring CNV from Single-Cell RNA-Seq
MubasherMohammed/pathml
Tools for computational pathology
MubasherMohammed/py-pgatk
Python tools for proteogenomics analysis toolkit
MubasherMohammed/python-cheatsheet
Comprehensive Python Cheatsheet
MubasherMohammed/raredisease
CG's rare disease pipeline in next flow, see the main repo here 👇
MubasherMohammed/scnanoseq
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
MubasherMohammed/scvelo
RNA Velocity generalized through dynamical modeling
MubasherMohammed/scvi-tools
Deep probabilistic analysis of single-cell omics data
MubasherMohammed/seurat
R toolkit for single cell genomics
MubasherMohammed/Single-cell-P.f-gametocyte
Analysis scripts and raw data of Gametocytes Sc-RNA-seq
MubasherMohammed/t.gondii_bmdc
MubasherMohammed/Tangram
Spatial alignment of single cell transcriptomic data.
MubasherMohammed/TOBIAS
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
MubasherMohammed/torchdrug
A powerful and flexible machine learning platform for drug discovery
MubasherMohammed/visium_heart
Spatial transcriptomics of heart tissue
MubasherMohammed/workshop-neural-nets-and-deep-learning
NBIS workshop in Neural Nets and Deep Learning