Shams's repositories
HumanBreast10X
Code for scRNA seq analysis Integration
CoefExplainer
Understand How to Interpret the Coefficients of a Categorical Linear Model
Cytoscape_workflows
collection of notebooks with different cytoscape workflows
deepimpute
An accurate and efficient deep learning method for single-cell RNA-seq data imputation
dev-kidney-snATAC
Codes used in the developmental kidney snATAC-seq data
dynbenchmark
Comparison of methods for trajectory inference on single-cell data 🥇
FigR
Functional Inference of Gene Regulation
gchromVAR
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
Hotspot_Analysis
Analysis scripts for writing the Hotspot paper
kerala_gov_hdi_comparison
Comparing HDI increase in kerala gov.
MetaNeighbor
A method to rapidly assess cell type identity using both functional and random gene sets
mrlocus
Mendelian Randomization of gene expression (exposure) on GWAS traits (outcome). See website for software usage guide:
open_chromatin
Repo for https://www.biorxiv.org/content/10.1101/427484v2
RaceID3_StemID2_package
Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data. This is a novel R package of the RaceID3 and StemID2 method including novel functionalities and performance improvements compared to the previous RaceID3/StemID2 version in the RaceID3_StemID2 repository. The RaceID3_StemID2 repository will not be updated anymore in the future.
scRNA-seq_topic_modeling
Single Cell RNA-seq Analysis by Topic Modeling
seurat-disk
Interfaces for HDF5-based Single Cell File Formats
SingleCellJugaad
These are the scripts used for common data manipulations in various single cell tools and analysis
SingleCells_SLE_paper
Scripts used for the analysis of single cell SLE PBMCs
SingleCellSignalR_v1
R package