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DeepTIL (Deep deconvolution of Tumor Infiltrating Leucocytes) quantifies the leukocyte composition of a sample. To achieve this, it combines Cibersort leucocyte fractions and total leukocyte abundance, calculated as normalized enrichment scores by AutoCompare_SES_norm.
DeepTIL can use either Cibersort-LM22 or Cibersort-LM7 to quantify the respectively 22 or 7 leukocyte subsets. The leukocyte abundance in a sample is computed by its sample enrichment score (SES) as depicted in ref. Briefly SES returns the -log(Pvalue) for testing (gene set rank distribution is greater than uniform distribution). To account for gene sets of different sizes, the raw SES are normalized on a 0-100 scale with 100 as maximal theoretical SES for the gene set size.
Citation :
When using DeepTIL to process data for publication please cite:
Assessment of tumor-infiltrating TCRVγ9Vδ2 γδ lymphocyte abundance by deconvolution of human cancers microarrays.
Marie Tosolini, Frédéric Pont, Mary Poupot, François Vergez, Marie-Laure Nicolau-Travers, David Vermijlen, Jean- Emmanuel Sarry, Francesco Dieli, Jean-Jacques Fournié . OncoImmunology , 2017 : 6;6(3).
Manual :
Single thread :
1- install Julia 1.7 or later (command line version) free programming language and install package :
CSV : add CSV
DataFrames : add DataFrames
ArgParse : add ArgParse
2- unzip the software
3- copy your Cibersort tables files in the “cibersort” directory.
- txt or csv files with TAB separator by default
- first line : column names
- first column : sample names (sample names must be strings, not numbers, othewise it produces a type error, Int instead of string)
- next columns : values with dot as decimal separator.
exemple :
4- copy your SES tables files in the “ses" directory. Tables must have ".tsv" extension. SES have to be calculated using the LM7 file as database in AutoCompare_SES_norm. Just copy the LM7 file in <Autocompare_SES_norm/databases/MyGeneSets/> for example, run Autocompare_SES_norm and get the SES files in <Autocompare_SES_norm/results_norm/>.
- txt or csv files with TAB separator by default
- first line : column names must contain the 7 folowing names : B, CD4, CD8, granulocytes, MoMaDC, NK, Tgd. Only those columns will be used for calculation.
- first column : sample names
- next columns : values with dot as decimal separator.
example :
5- execute the software by the command :
julia deeptil-005.jl -f CIBERSORT_file -e SES_file
example :
julia deeptil-005.jl -f cibersort/CIBERSORT_LM7_GSEXX.txt -e ses/SES_LM7_GSEXX.tsv
6- the results are in the results directory.
Parallel file processing (linux only) :
This version is usefull to process many Cibersort and SES files in parallel.
Same installation and procedure than for single CPU.
1- install GNU parallel and Perl
2- very important Cibersort and SES file names must be formated as follows :
CIBERSORT.samplename.txt
SES_samplename_norm.tsv
do not remove the dot after CIBERSORT !
3- execute the software by the command :
perl parallel_deeptil-05.pl nb_of_cpus
example :
perl parallel_deeptil-05.pl 10 # parallel computing of 10 files on 10 cpus
4- the results are in the results directory.
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