Pinned Repositories
Enrichment-Analysis
From RNA-seq raw reads to enriched pathways by DEGs
Methylation_Analysis
Comprehensive tutorial for differential methylation analysis, differential variability analysis and integrative analysis
pipeline_whole_exome_sequencing_analysis
The snakemake workflow for whole-exome sequencing analysis and generating vcf files
RNA-seq-differential-expression
Differential gene expression analysis on RNA-seq data
RNA-seq-survival-analysis
Survival analysis on gene expression (RNA-seq) in bladder cancer TCGA data
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)
scRNA_seq-analysis
scRNA analysis of public dataset on bladder cancer
scRNA_velocity_analysis
scRNA velocity analysis using Seurat, velocyto and scvelo
sequencing_benchmark_datasets
A repo on datasets used in Sequencing benchmarked study, Nat Biotech, September 2021
hamidghaedi's Repositories
hamidghaedi/pipeline_whole_exome_sequencing_analysis
The snakemake workflow for whole-exome sequencing analysis and generating vcf files
hamidghaedi/bladder-cancer-subtyping-Machine_learning
IHC based classifier to predict major subtypes of bladder cancer:
hamidghaedi/mutation_clustering
Somatic Mutation data Clustering
hamidghaedi/REdiscoverTE
A pipeline to run REdiscoverTE tool on paired-end fastq files and creating expression matrix for genes and TEs (transposon elements)
hamidghaedi/awk_for_genomics_data_science_tutorial
A collection of awk one-liner helpful in genomic data science
hamidghaedi/cancer_origin_prediction
A deep learning approach to predict origin of cancer based on DNA methylation profile
hamidghaedi/cancer_origin_prediction-1
Predict cancer tissue of origin using DNN-based methylation model
hamidghaedi/ClinVar
XGBoost classifiers to predict variant classification conflict
hamidghaedi/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
hamidghaedi/GSEA_app
hamidghaedi/modern_stat_4_modern_biology
A worksheet for Modern Statistics for Modern Biology book
hamidghaedi/oncomineGenes2Pathway
Mapping genes in the Oncomine Comprehensive Assay v3 (ocav3) to KEGG pathways
hamidghaedi/Running_Jupyter_NB_compute-canada-hpc
Beginner tutorials and help for using Compute Canada's High Performance Computer. Learn to setup and run a Jupyter Notebook!
hamidghaedi/somatic_variant_calling_gatk_Mutect2
Somatic variant calling using Mutect2
hamidghaedi/TE_element_correlation
hamidghaedi/TE_expression_BLCA
hamidghaedi/tutorial_DESeq2_contrasts