Hamid Ghaedi's repositories
Enrichment-Analysis
From RNA-seq raw reads to enriched pathways by DEGs
RNA-seq-survival-analysis
Survival analysis on gene expression (RNA-seq) in bladder cancer TCGA data
Methylation_Analysis
Comprehensive tutorial for differential methylation analysis, differential variability analysis and integrative analysis
scRNA_seq-analysis
scRNA analysis of public dataset on bladder cancer
RNA-seq-differential-expression
Differential gene expression analysis on RNA-seq data
Unsupervised_Clustering_for_Gene_Expression_data
Cancer subtype discovery using consensus clustering approach to find pattern in expression data (RNA-seq)
scRNA_velocity_analysis
scRNA velocity analysis using Seurat, velocyto and scvelo
scRNA-cell-cell-communication-analysis
A repo on cell-cell interaction inference in scRNA dataset
scRNA_cell_annotation
Assigning cell labels w/o ref data (Tabula Sapiens)
sequencing_benchmark_datasets
A repo on datasets used in Sequencing benchmarked study, Nat Biotech, September 2021
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
DNA-seq-pipeline
A repo on DNA-seq pipleine for somatic mutation calling and annotation
file_sharing
repo for sharing fils
gdc-workflow-overview
Overview of GDC Harmonization Workflows
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
scTE
scTE updated version
Transposons_Exp_BLCA
A project on quantifying expression level of TEs in bladder cancer tissue samples
Useful-Tools-and-Resources
A repo to collect a list of useful tools for data analysis