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single-cell-multi-omics-profiling-of-human-gliomas

Code for Chaligne, Gaiti, Silverbush, Schiffman et al. paper “Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states”

single-cell-papers-with-code

Papers with code for single cell related papers

singlecellrna_melanoma_paper

snakemake-cartesian-ddg

Snakemake pipeline for Rosetta 'cartesian-ddg' protocol for protein stability prediction upon mutations.

snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

snap-seq

Computer code for the snAP-seq manuscript

snapatac

Analysis Pipeline for Single Cell ATAC-seq

snaptron

fast webservices based query tool for large sets of genomic features

snrna-seq

R scripts for single nuclei RNA seq analysis

snrnaseq_adipocyte

The following repository contains code for all scRNAseq analysis and visualization performed in the paper: "Multidimensional Single-Nuclei RNA-Seq Reconstruction of Adipose Tissue Reveals Mature Adipocyte Plasticity Underlying Thermogenic Response

software

Software developed at the Max Planck Institut für Eisenforschung

spliceai

A deep learning-based tool to identify splice variants

splicelauncher

RNAseq pipeline for alternative splicing junctions

splicing_project

splicingincancer

subread_to_dexseq

Scripts to import your FeatureCounts output into DEXSeq

superdopebioinformatics

CMU 03713 group project for Spring 2020

szs_pipeline

Code to calculate the Splicing Z Score (SZS) for single cell RNA-seq splicing analysis

theme-next-docs

The documentation for NexT.

top-ai-conferences-paper-with-code

This repository is a collection of AI top conferences papers (e.g. ACL, EMNLP, NAACL, COLING, AAAI, IJCAI, ICLR, NeurIPS, and ICML) with open resource code

transindel

Indel caller for DNA-seq or RNA-seq

trust4

TCR and BCR assembly from RNA-seq data

twint

An advanced Twitter scraping & OSINT tool written in Python that doesn't use Twitter's API, allowing you to scrape a user's followers, following, Tweets and more while evading most API limitations.

u1-snrna

ucscxenashiny

📊 An R package for interactively exploring UCSC Xena https://xenabrowser.net/datapages/

ui

Front-end for Cellenics

varid_analysis

VarID analysis of murine hematopoietic progenitors and intestinal epithelial cells. VarID is part of RaceID v0.1.4

viral-mutation

Language modeling of viral evolution

viscap

VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number variants (CNVs) from targeted next-generation sequencing data. For algorithmic details, see Pugh TJ et al. Genet Med. 2016 Jul;18(7):712-9.

visualizingdestimulatedexons

Internship on visualizing the differential expression of stimulated exons