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atac_rna_tonsils

The analysis pipeline to accompany the manuscript "Integrated single-cell transcriptomics and epigenomics reveals strong germinal center-associated etiology of autoimmune risk loci"

benniger_tf_regulators

Analysis to accompany "Dynamic changes in β-cell [Ca 2+ ] regulates NFAT activation, gene transcription and islet gap junction communication" published in Molecular Metabolism

bulk_rnaseq

A basic pipeline for initial processing of bulk RNA seq data

clipper

A tool to identify CLIP-seq peaks

dog_behavior_tracker

A repository containing an R shiny app that generates a fillable form to track dog behavior. This automatically updates a sheet on google drive

eclip_idr

A snakemake pipeline to run idr on eclip replicates

eclip_normalization

rewriting the eclip normalization to work with R1 input

monocle-release

mtec.10x.pipeline

R package with all necessary functions to reproduce analysis for the eLife publication Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells"

mtec_analysis

The snakemake pipelines to accompany the eLife publication titled "Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells"

myexamplerepo

This repository is an example for submitting code to github

pdba_files

scopfunctions

An R package of functions for single cell -omics analysis.

single_cell_scripts

sussel_rnaseq_ptpn

Analysis of the PTPN experiment with Yong Kim

velocyto.py

RNA velocity estimation in Python

visium_ovarian_cancer

All code needed to reproduce analysis in Small cell carcinoma of the ovary hypercalcemic type (SCCOHT): A review and novel case with dual germline SMARCA4 and BRCA2 mutations

visium_public_shiny

The shiny app for the visium data