hamidghaedi Goto Github PK

50algorithms

atac-seq

Pipeline to download, process and analyze TCGA bladder cancer ATAC-seq data on HPC environment

awk_for_genomics_data_science_tutorial

A collection of awk one-liner helpful in genomic data science

bladder-cancer-subtyping-machine_learning

IHC based classifier to predict major subtypes of bladder cancer:

cancer_origin_prediction

A deep learning approach to predict origin of cancer based on DNA methylation profile

cancer_origin_prediction-1

Predict cancer tissue of origin using DNN-based methylation model

causalnex

A Python library that helps data scientists to infer causation rather than observing correlation.

cbioportal-local-deployment

Steps into local deployment of cBioPortal using Docker on a Win machine

clinvar

XGBoost classifiers to predict variant classification conflict

deep_learning_for_structured_data

Production repo to accompany Deep Learning with Structured Data book from Manning: https://www.manning.com/books/deep-learning-with-structured-data

dna-seq-pipeline

A repo on DNA-seq pipleine for somatic mutation calling and annotation

enrichment-analysis

From RNA-seq raw reads to enriched pathways by DEGs

file_sharing

repo for sharing fils

gdc-workflow-overview

Overview of GDC Harmonization Workflows

gsea_app

hamidghaedi

harmony

Harmony framework for connecting scRNA-seq data from discrete time points

hetexc_intervals

Identification and annotation of HetExc regions in human genome hg38

hw_equilibrium_violation

Identifying regions in exomes with excess of heterozygotes

identify_critical_aa_using_esm-variant

Using ESM-variant to identify critical residues in a protein, needed to assign PM1 criteria to a variant

keggpath2gene_path2modules

R script to map gene name to each KEGG pathways and Modules

llm-course

Course to get into Large Language Models (LLMs) with roadmaps and Colab notebooks.

machine-learning-for-proteins

Listing of papers about machine learning for proteins.

maftools

customization of the original package

metacell_by_supercell

Using SuperCell to define meta cell in sc datasets

methylation_analysis

Comprehensive tutorial for differential methylation analysis, differential variability analysis and integrative analysis

modern_stat_4_modern_biology

A worksheet for Modern Statistics for Modern Biology book

mutation_clustering

Somatic Mutation data Clustering

oncominegenes2pathway

Mapping genes in the Oncomine Comprehensive Assay v3 (ocav3) to KEGG pathways

pipeline_whole_exome_sequencing_analysis

The snakemake workflow for whole-exome sequencing analysis and generating vcf files