Shams (kvshams)

kvshams

Geek Repo

Company:Broad Institute and Harvard Medical School

Location:Boston

Home Page:https://scholar.google.com/citations?hl=en&user=z5xB0agAAAAJ&view_op=list_works&sortby=pubdate

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Shams's repositories

HumanBreast10X

Code for scRNA seq analysis Integration

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bayNorm

Normalization for single cell RNA-seq data

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cisTopic

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

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CoefExplainer

Understand How to Interpret the Coefficients of a Categorical Linear Model

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Cytoscape_workflows

collection of notebooks with different cytoscape workflows

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deepimpute

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

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dev-kidney-snATAC

Codes used in the developmental kidney snATAC-seq data

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dynbenchmark

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

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FigR

Functional Inference of Gene Regulation

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gchromVAR

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

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Hotspot_Analysis

Analysis scripts for writing the Hotspot paper

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kerala_gov_hdi_comparison

Comparing HDI increase in kerala gov.

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MELD

Quantifying experimental perturbations at single cell resolution

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MetaNeighbor

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

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MIMOSCA

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

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mrlocus

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

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One2One

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

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open_chromatin

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

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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.

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scMatch

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

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scRNA-seq_topic_modeling

Single Cell RNA-seq Analysis by Topic Modeling

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seurat-disk

Interfaces for HDF5-based Single Cell File Formats

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SingleCellJugaad

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

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SingleCells_SLE_paper

Scripts used for the analysis of single cell SLE PBMCs

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