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als_spinalcord_qtls

Data Portal for NYGC ALS Spinal Cord

biscuit

BISulfite-seq CUI Toolkit

biscuit_snakemake_workflow

Snakemake Workflow For Running Biscuit https://github.com/huishenlab/biscuit

biscuiteer

tools for analysing Biscuit (https://huishenlab.github.io/biscuit/) output

candles

Data + code examples used here: https://twitter.com/kate_ptrv/status/1332398737604431874?s=20

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

data202

Class notes, datasets, project details, other information from DATA-202, Information Systems & Data Management, Fall 2020.

expansionhunter

A tool for estimating repeat sizes

gatk-sv

A structural variation pipeline for short-read sequencing

geneimpacts

prioritize effects of variant annotations from VEP, SnpEff, et al.

ggpackets

Cleaner composition of ggplot layers

glmmseq

Gene-level general linear mixed model

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

lab08-template

mi-covid-viz

Create a visual of Michigan Covid Cases

miniwdl

Workflow Description Language developer tools & local runner

pathexplore

Gene Set Enrichment Clustering Plots

pbspretty

colorful, descriptive alternatives to pbsnodes and qstat

proj-westra-data202

Walking through the analysis and a figure from a Nature Genetics article, replicating the lab's findings that mutations in genes are enriched based on specific exposures. || Data 202 Final Project, Fall 2020.

qsubtools

r4ds

R for data science: a book

rnaseq_workflow

snakemake workflow for bulk RNA-seq workflow using STAR-edgeR

sbatchtools

sbatchtools is a suite of shell scripts to automate slurm submissions (based on www.github.com/LeeLMarshall/qsubtools)

sc-type

sccustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

scdblfinder

Methods for detecting doublets in single-cell sequencing data

scgate

marker-based purification of cell types from single-cell RNA-seq datasets

scientific_python_cheat_sheet

simple overview of python, numpy, scipy, matplotlib functions that are useful for scientific work

scrna-seq_online

seurat

R toolkit for single cell genomics