kvshams

bayNorm

Normalization for single cell RNA-seq data

Bioinfo2019

cisTopic

cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

Clint_Coronary_snATAC_natureGenetics

CNA_combined_with_ML

Code to compute network properties (features) for subgraphs of a correlation-based network

CoefExplainer

Understand How to Interpret the Coefficients of a Categorical Linear Model

conquer_comparison

Code for evaluation of differential expression methods in single-cell RNA-seq data

Cytoscape_workflows

collection of notebooks with different cytoscape workflows

HumanBreast10X

Code for scRNA seq analysis Integration

Lymph_node_project

List of all R codes used for the analysis of single cell data in the paper Blecher et al. on the study of immune cell communications.

kvshams/HumanBreast10X

Code for scRNA seq analysis Integration

kvshams/bayNorm

Normalization for single cell RNA-seq data

kvshams/cisTopic

cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

kvshams/Clint_Coronary_snATAC_natureGenetics

kvshams/CoefExplainer

Understand How to Interpret the Coefficients of a Categorical Linear Model

kvshams/Cytoscape_workflows

collection of notebooks with different cytoscape workflows

kvshams/deepimpute

An accurate and efficient deep learning method for single-cell RNA-seq data imputation

kvshams/dev-kidney-snATAC

Codes used in the developmental kidney snATAC-seq data

kvshams/dynbenchmark

Comparison of methods for trajectory inference on single-cell data 🥇

kvshams/FigR

Functional Inference of Gene Regulation

kvshams/ft-lab

kvshams/gchromVAR

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

kvshams/Hotspot_Analysis

Analysis scripts for writing the Hotspot paper

kvshams/Image-based-cell-profiling-enhancement-via-data-cleaning-methods

kvshams/intro-to-python-cwml-workshop

kvshams/kerala_gov_hdi_comparison

Comparing HDI increase in kerala gov.

kvshams/MELD

Quantifying experimental perturbations at single cell resolution

kvshams/MetaNeighbor

A method to rapidly assess cell type identity using both functional and random gene sets

kvshams/MIMOSCA

A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.

kvshams/mrlocus

Mendelian Randomization of gene expression (exposure) on GWAS traits (outcome). See website for software usage guide:

kvshams/NCOMMS-20-00614

kvshams/One2One

This package is used to get 1:1 orthologs based on MGI homology data from http://www.informatics.jax.org/homology.shtml

kvshams/open_chromatin

Repo for https://www.biorxiv.org/content/10.1101/427484v2

kvshams/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.

kvshams/scMatch

scMatch: a single-cell gene expression profile annotation tool using reference datasets

kvshams/scRNA-seq_topic_modeling

Single Cell RNA-seq Analysis by Topic Modeling

kvshams/seurat-disk

Interfaces for HDF5-based Single Cell File Formats

kvshams/SingleCellJugaad

These are the scripts used for common data manipulations in various single cell tools and analysis

kvshams/SingleCells_SLE_paper

Scripts used for the analysis of single cell SLE PBMCs

kvshams/SingleCellSignalR_v1

R package