Discover crazyhottommy/Epigenome_RoadTrip Open Source project

RNAseq analysis notes from Ming Tang

1,143

RNA-seq-analysis

ChIP-seq analysis notes from Ming Tang

867

ChIP-seq-analysis

scRNAseq analysis notes from Ming Tang

670

scRNAseq-analysis-notes

626

bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

452

awesome_spatial_omics

tools and notes for spatial omics

209

The-world-of-faculty

resources for faculty

207

TCR-BCR-seq-analysis

T/B cell receptor sequencing analysis notes

202

DNA-seq-analysis

DNA sequencing analysis notes from Ming Tang

my notes for scATACseq analysis

139

scATACseq-analysis-notes

113

pyflow-ChIPseq

a snakemake pipeline to process ChIP-seq files from GEO or in-house

Single Cell Cluster Evaluation

101

scclusteval

pyflow-ATACseq

ATAC-seq snakemake pipeline

DNA methylation analysis notes from Ming Tang

DNA-methylation-analysis

machine-learning-resource

papers_with_data_to_mine

published papers with a lot of data

oneliner_100day_challenge

Bioinformatics one-liner for 100 days

scATACutils

R/Bioconductor package for working with 10x scATACseq data

scRNA-seq-workshop-Fall-2019

Harvard FAS informatics scRNAseq workshop website

biotech_resource

some resources for startup companies

compbio_tutorials

My youtube programming scripts

RNAseq pipeline based on snakemake

compbio_resources_chatomics

pyflow-RNAseq

tools and notes for long reads analysis

Machine_learning_drug_discovery

awesome-long-reads

pyflow-scATACseq

snakemake workflow for post-processing scATACseq data

python scripts for the Coursera Bioinformatics for Beginners

crazyhottommy

Coursera_Bioinformatics_for_Beginners

A Snakemake pipeline for cellranger to process 10x single-cell RNAseq data

pyflow-cellranger

scripts-general-use

cluster stability measurement by subsampling and reclustering with Seurat V3 and V4

single-cell-DNAseq-notes

pyflow_seurat_parameter

immunotherapy_scRNAseq_papers

my CV using pagedown

JavaScript

awesome-single-cell-proteomics

mixed_histology_lung_cancer

cloud_computing_resources

MIT6.00.1x-Introduction-to-Computer-Science-and-Programming-Using-Python

my notes for the homework

single-cell RNAseq ATACseq processing pipeline

immunology_tools

pyflow-single-cell

R, python, unix tools for 10x scATACseq data

writing-tips

scATACtools

wholebrain_docker

docker file for wholebrain http://www.wholebrainsoftware.org/cms/installing-wholebrain-on-ubuntudebian/

Dockerfile

Genrich_compare

snakemake workflow comparing Genrich and MACS2

Automatically exported from code.google.com/p/phantompeakqualtools

phantompeakqualtools

computation_wiki

Tommy's computation wiki

flowcytometry_analysis_notes

mixing_histology_lung_cancer

snakemake workflow for random forest based feature selection on chromHMM data

pyflow-chromForest

my dot files on Harvard Odyssey HPC

odyssey_dot_files

batch design primers for scATACseq differential peaks

primer3_scATAC_peaks

docker file for seurat v3

seurat_v3_dockerfile

Dockerfile

PRADA_pipeline_Verhaak_lab

docker file to extend rocker tidyverse

STAT115_HW

Tommy's homework

rocker_tidyvese_jpeg_cairo

Dockerfile

ucn3_neuron_microarray_analysis

epigenomics_concept_learning

CIDC_single_cell

snakemake single cell pipeline for CIDC

examples for using scclusteval

ucn3_neuron_microarray

EvaluateSingleCellClustering

bulk-RNAseq-workshop

compbio_challenges

machine_learning_datasets

rosalind_problems_python_solutions

data-science-machine-learning-project

Development of the ChIPseq workshop for Data Carpentry

ChIP-seq-carpentry