piquelab Goto Github PK

aloft_puberty

aloft_rna-seq

code used to generate results in Resztak et al, 2020

ase

Source code for Allelic Specific Expression Algorithm

asepipeline

Simplified ASE pipeline using samtools pileup and Quasar.

bc_classroom_rstudio

bc_grid_rstudio_server

RStudio Server app for Open OnDemand

caffeine_bit-starr-seq

Scripts from https://www.biorxiv.org/content/10.1101/2022.11.22.517533v1.full

circuitsnps

counts_cellranger

General script to run cellranger counts.

counts_cellranger_atac

General script to run cellranger-atac counts.

covid19placenta

Maternal-Fetal Immune Responses in Pregnant Women Infected with SARS-CoV-2

demux_cellranger_brain

Demultiplexing pipeline with demuxlet for the brain project (hg38)

demux_cellranger_gp

Demultiplexing pipeline with demuxlet for the guinea pig project

demux_cellranger_preeclampsia

Demultiplexing pipeline with demuxlet for the preeclampsia project (hg38)

gxe_browser

Code for the GxE browser website

gxe_pipeline

Workflow for the Gene Environment Interaction project

gxenet

GxE Networks Browser

gxexc

Scripts used to analyzed data from exposing LCLs, IPSCs, and CMs to 28 treatments, as detailed in Findley et al (2021).

gxp-code

This repository contains all scripts files of the GxP project

il9scrna

The single-cell analysis of Il9 mouse model

labs

Rmd source files for the HarvardX series PH525x

mesh

multiclasslr

multinomial logistic regression model for MESH output

murine_scrna

The single-cell atlas of the murine reproductive tissues during preterm labor

myometrium-analysis

Single cell myometrium analysis

parturition_paper

parturitionmyometrium

Single-Cell Atlas of Human Parturition: The Myometrium

polygenicadaptationcode

popgen-notes

Population genetics notes from Graham Coop

progress-covid-19

Scripts to monitor progress of COVID-19