Repositories list

• GxM_IBD

  Public
  0•0•0•0•Updated Feb 17, 2025Feb 17, 2025

• QuASAR2

  Public
  Quantitative Allele Specific Analysis of Reads. Joint genotyping & ASE inference for RNA-seq data

  R

  •

  MIT License

  •10•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• Il9scRNA

  Public
  The single-cell analysis of Il9 mouse model

  R

  •

  MIT License

  •1•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• sc_multiome

  Public
  R

  •1•0•0•0•Updated Jan 8, 2025Jan 8, 2025

• ArchR

  Public
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

  R

  •

  MIT License

  •141•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• sc-atac

  Public
  single cell ATAC data analysis

  R

  •

  MIT License

  •0•0•0•0•Updated Dec 5, 2024Dec 5, 2024

• counts_cellranger

  Public
  General script to run cellranger counts.

  Shell

  •1•2•0•0•Updated Jun 21, 2024Jun 21, 2024

• fastdemux

  Public
  Demultiplexing by genotype

  C

  •

  MIT License

  •0•0•1•0•Updated May 8, 2024May 8, 2024

• counts_cellranger_atac

  Public
  General script to run cellranger-atac counts.

  Shell

  •1•1•0•0•Updated May 3, 2024May 3, 2024

• bc_grid_rstudio_server

  Public
  RStudio Server app for Open OnDemand

  Shell

  •

  MIT License

  •8•0•0•0•Updated Apr 23, 2024Apr 23, 2024

• sc_brains

  Public
  single cell brain project

  R

  •0•1•0•0•Updated Mar 20, 2024Mar 20, 2024

• locoglimpse2

  Public
  Low coverage imputation using GLIMPSE2 in the grid

  Shell

  •0•0•0•0•Updated Mar 2, 2024Mar 2, 2024

• GxP-code

  Public
  This repository contains all scripts files of the GxP project

  R

  •0•0•0•0•Updated Feb 28, 2024Feb 28, 2024

• Caffeine_BiT-STARR-Seq

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

  R

  •0•0•0•0•Updated Feb 20, 2024Feb 20, 2024

• popgen-notes

  Public
  Population genetics notes from Graham Coop

  Jupyter Notebook

  •

  MIT License

  •128•0•0•0•Updated Feb 12, 2024Feb 12, 2024

• scaip

  Public
  Single Cell Asthma Immunology Project

  R

  •

  MIT License

  •0•2•0•0•Updated Jan 9, 2024Jan 9, 2024

• Parturition_paper

  Public
  R

  •

  MIT License

  •1•3•0•0•Updated Dec 7, 2023Dec 7, 2023

• covid19placenta

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

  R

  •

  MIT License

  •0•0•0•0•Updated Dec 7, 2023Dec 7, 2023

• asepipeline

  Public
  Simplified ASE pipeline using samtools pileup and Quasar.

  R

  •

  MIT License

  •1•0•0•0•Updated Jun 21, 2023Jun 21, 2023

• SCAIP-genetic

  Public
  R

  •0•1•0•0•Updated May 30, 2023May 30, 2023

• demux_cellranger_preeclampsia

  Public
  Demultiplexing pipeline with demuxlet for the preeclampsia project (hg38)

  Shell

  •3•0•0•0•Updated May 26, 2023May 26, 2023

• demux_cellranger_gp

  Public
  Demultiplexing pipeline with demuxlet for the guinea pig project

  Shell

  •3•0•0•0•Updated Dec 2, 2022Dec 2, 2022

• murine_scRNA

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

  R

  •

  MIT License

  •1•1•0•0•Updated Nov 18, 2022Nov 18, 2022

• bc_classroom_rstudio

  Public
  HTML

  •

  MIT License

  •1•0•0•0•Updated Sep 27, 2022Sep 27, 2022

• ALOFT_puberty

  Public
  R

  •0•0•0•0•Updated Sep 18, 2022Sep 18, 2022

• demux_cellranger_brain

  Public
  Demultiplexing pipeline with demuxlet for the brain project (hg38)

  Shell

  •3•1•0•0•Updated Apr 17, 2022Apr 17, 2022

• myometrium-analysis

  Public
  Single cell myometrium analysis

  R

  •0•0•0•0•Updated Mar 23, 2022Mar 23, 2022

• ParturitionMyometrium

  Public
  Single-Cell Atlas of Human Parturition: The Myometrium

  R

  •

  MIT License

  •0•0•0•0•Updated Nov 24, 2021Nov 24, 2021

• Viral-Track

  Public
  R

  •27•0•0•0•Updated Sep 10, 2021Sep 10, 2021

• GxExC

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

  R

  •

  MIT License

  •0•1•0•0•Updated Jan 29, 2021Jan 29, 2021