marencc Goto Github PK

mutation_analysis_scripts

day to day activity for mutation data

orchestratingsinglecellanalysis

Content for the OSCA Book.

palantir

Single cell trajectory detection

pca_demo

plotting_in_r

progds-2-20201-pac4_jan2022

pseudoreferencepipeline

SLURM-based pipeline for alignment, variant calling, and generation of pseudoreference FASTAs from Illumina data (DNA- or RNAseq)

pyladies_vienna_data_course

Materials for PyLadies Vienna Data course, inspired by PyLadies Czech Republic

python-programming-exercises

100+ Python challenging programming exercises

pythondatasciencehandbook

Python Data Science Handbook: full text in Jupyter Notebooks

r-workshop-1

R workshop from 1/26/18

rclone_jobber

An rclone script to perform backups

rcourse

Reproducible Quantitative Methods for EEB

resources_for_private_and_secure_ai

Resources for private and secure Machine Learning and Artificial Intelligence

riboseed

pipeline for using ribosomal flanking regions to improve bacterial genome assembly

rna-seq-kallisto-sleuth

A workflow for RNA-seq differential expression analysis based on Kallisto and Sleuth.

rnaseq

RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control

rnaseq_trinity_tuxedo_workshop

materials for the RNA-Seq workshop on Trinity and Tuxedo, covering de novo and genome-guided transcript assembly and downstream analysis.

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rshiny-tutorial

rtutorial

Tutorials on R, CBioPortal (cgdsr), CellMiner (rcellminer), and Pathway Commons (paxtoolsr)

ru_atacseq

ru_rnaseq

ru_tidyverse

The Rockefeller University tidyverse workshop

sarek

Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing

scrna-seq_sep2019

V_2019

scrna.seq.course

Analysis of single cell RNA-seq data course

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

seurat

R toolkit for single cell genomics

shell-novice

The Unix Shell