GitHub - mahogny/th2crispr: An unbiased reconstruction of the T helper cell type 2 differentiation network

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An unbiased reconstruction of the T helper cell type 2 differentiation network

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Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
ext_chip2		ext_chip2
screen		screen
tflist		tflist
thexpress		thexpress
README		README
analyze_atacvst.R		analyze_atacvst.R
analyze_chip.R		analyze_chip.R
analyze_ko4.R		analyze_ko4.R
analyze_ko_deseq.R		analyze_ko_deseq.R
analyze_ko_factortest.R		analyze_ko_factortest.R
analyze_newatac.R		analyze_newatac.R
analyze_newscreenqc.R		analyze_newscreenqc.R
analyze_oe_DE.R		analyze_oe_DE.R
analyze_oe_actdiff.R		analyze_oe_actdiff.R
analyze_oe_chip.R		analyze_oe_chip.R
analyze_oe_chipgraph.R		analyze_oe_chipgraph.R
analyze_oe_clusterchip.R		analyze_oe_clusterchip.R
analyze_oe_indgenes.R		analyze_oe_indgenes.R
common_geneid.R		common_geneid.R
common_gotest.R		common_gotest.R
common_readrnaatacchip.R		common_readrnaatacchip.R
crispr_complexity_analysis.R		crispr_complexity_analysis.R
map_jasparname_sym.csv		map_jasparname_sym.csv
map_ortho_humanmouse.csv		map_ortho_humanmouse.csv
mappingScreenNames.txt		mappingScreenNames.txt
mouse_human_ortholog.csv		mouse_human_ortholog.csv
process_analyzemara2.R		process_analyzemara2.R
process_aracne2.R		process_aracne2.R
process_aracne_out.R		process_aracne_out.R
process_atac_coloc.R		process_atac_coloc.R
process_impc.R		process_impc.R
process_makemara.R		process_makemara.R
process_runmageck.R		process_runmageck.R
process_runstan.R		process_runstan.R
process_runstan_batch.R		process_runstan_batch.R
process_runstan_test.R		process_runstan_test.R
process_screenqc.R		process_screenqc.R
process_storewebsite.R		process_storewebsite.R
process_tcDE.R		process_tcDE.R
round2indko.R		round2indko.R

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This code belongs to the paper
"An unbiased reconstruction of the T helper cell type 2 differentiation network"
by J. Henriksson et al.

Corresponding author: Sarah Teichmann, [email protected]

But for technical questions, consider going straight to Johan Henriksson: [email protected]

The code provided here is not sufficient to reproduce the article from the raw data - too many BASH scripts
and Makefiles are scatted over the EBI cluster, with paths that only make sense in that environment.
However, this code should be more or less complete if count tables are provided

The code is available under the 2-clause BSD license. However, should you find a signicant part useful, please cite our
paper (or add a reference in your code).