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10x-scatac-2019

Code Repository for Satpathy Granja et al 2019

atac-seq-pipeline

ENCODE ATAC-seq pipeline

awesome-single-cell

List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

bioc2020workshop

biocnyc

Materials presented at the BiocNYC meet-up

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

cellphonedb

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

chromvarmotifs

R package with motifs for use with chromVAR

deeptools

Tools to process and analyze deep sequencing data.

imcsegmentationpipeline

A pixelclassification based multiplexed image segmentation pipeline

lollipops

Lollipop-style mutation diagrams for annotating genetic variations.

macs

MACS -- Model-based Analysis of ChIP-Seq

magic

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

mdlabbook

mdlabbook is a markdown-format lab notebook

midnight

Midnight is a Jekyll theme for GitHub Pages

ngs_course

Course on analysis of NGS data (RNA-Seq. and ATAC-Seq.) using Galaxy

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

nichenetr

NicheNet: predict active ligand-target links between interacting cells

pik3ca_mg_analysis

A code and script depository for the analysis in Blanpain Lab, regarding the project studying multipotency upon oncogenic stress

posterdown

Use RMarkdown to generate PDF Conference Posters via HTML

powsimr

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

project-template

Template for project directory structure.

pten_codes

Codes for analysis and plotting on the paper

r-course_2021summer

r-coursework

R notebook and example data for beginner :)

seqtk

Toolkit for processing sequences in FASTA/Q formats

seurat

R toolkit for single cell genomics

severo.jl

a software package for analysis and exploration of single-cell RNA-seq datasets

thesis_academic

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms