/sclinker-skg

Primary LanguageShell

sclinker-skg

Setup

  1. Prerequisite
  • gsutil
  • conda
  • scanpy (in python3)
  • bedtools
  • R (calling /usr/bin/Rscript in the script.)
  • tidyverse (in R)
  1. Download data
git clone https://github.com/yyoshiaki/sclinker-skg.git
cd sclinker-skg
bash scripts/prep_data.sh ${PWD}
  1. create env for ldsc
cd ldsc
conda env create --file environment.yml
conda create --name scanpy1.8.1 python=3.8 scanpy=1.8.1

sclinker-celltype

This includes scanpy's scanpy.tl.rank_genes_group.

Usage

bash ./scripts/sclinker-workflow.celltype.skg.sh ./configs/pbmc_all.sh

Example (PBMC)

mkdir -p example
cd example
# download scanpy object
wget https://storage.googleapis.com/broad-alkesgroup-public/LDSCORE/Jagadeesh_Dey_sclinker/scdata/pbmc-processed-annotated.h5ad
cd ..

bash ./scripts/sclinker-workflow.celltype.skg.sh ./configs/pbmc_all.sh

input

BASEDIR=~/yyoshiaki-git/sclinker-skg

NAME=exmaple.pbmc.all
CELLTYPE_COL=celltype
WORKDIR=$BASEDIR/$NAME
ADATA=$BASEDIR/example/pbmc-processed-annotated.h5ad
# 0 for all genes, >=1 to select top n gene for each celltype
N_TOP_GENE=0
TISSUE=BLD # BLD, BRN
CSV_SUMSTATS=${BASEDIR}/data/ldsc/sumstats.csv

sclinker-genescores

This pipline starts from a genescore's CSV file.

bash ./scripts/sclinker-workflow.genescores.skg.sh ./configs/pbmc_all.genescores.sh

Example (PBMC, after execution of celltype mode)

bash ./scripts/sclinker-workflow.genescores.skg.sh ./configs/pbmc_all.genescores.sh

input

BASEDIR=~/yyoshiaki-git/sclinker-skg

NAME=exmaple.pbmc.genescores.all
WORKDIR=$BASEDIR/$NAME
GENE_SCORES=$BASEDIR/example.pbmc.all/celltype_genescores.csv
# 0 for all genes, >=1 to select top n gene for each celltype
N_TOP_GENE=0
TISSUE=BLD # BLD, BRN
CSV_SUMSTATS=${BASEDIR}/data/ldsc/sumstats.csv