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10x-scatac-2019

Code Repository for Satpathy Granja et al 2019

10x-scrnaseq

Shell and R scripts used to process single-cell RNAseq files using the 10X library construction kit

10x_atacseq

10xmapping

mapping somatic variants to cell barcodes in scRNA-Seq data

atac_mito_sc

single cell ATACseq pipeline

bedtools2

bedtools - the swiss army knife for genome arithmetic

bpscrnaseq

cb_sniffer

mutation(barcode) caller for 10x single cell data

cdips_tutorial_2017

Tutorial on Data Manipulation in Python

cellsnp

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

cerebra

finds mutants in your scRNA-seq experiment

cerebro

Visualize scRNA-seq results.

clonealign-pipeline

A pipeline to process scRNA-seq (10X chromium) and scDNA-seq CNV data and infer clone-specific expression using clonealign

clustering-algorithms

Focusing on 3 key methods (UMAP, t-SNE, scVI) by using scRNA-seq data

conos

Clustering on Network of Samples

coursera-bioinformatics

My solution to Bioinformatics Specialization (Finding Hidden Messages in DNA; Genome Sequencing; Comparing Genes, Proteins, and Genomes; Molecular Evolution; Genomic Data Science and Clustering; Finding Mutations in DNA and Proteins; Bioinformatics Capstone: Big Data in Biology)

ctat-mutations

Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19

emblem

epic

Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.

flypn

Workflows and analysis of scRNA-seq of Olfactory Projection Neurons for Li, Horns et al. (2017)

github-scrnaseq-cortexdata

Analysis of early neurogenesis development data from droplet sequencing

gse76275-tnbc

harmony

Harmony framework for connecting scRNA-seq data from discrete time points

human_macrophage_project

scripts for analyzing data of macrophage development in human

icellr

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq and CITE-seq).

ihcount

IHC-image analysis workflow

immunedeconv

A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter)

immuno_notes

Immunology-related bioinformatics data and tools

in-depth-ngs-data-analysis-course

Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.

klunctions

useful functions for scRNA-seq analysis