- Complete set of multi-threaded genomics utilities for ensembl and differential expression matrix.
human genomics utilities.
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Gaurav Sablok, IBCH, PAN, Poznan, Poland,
https://portal.ichb.pl/laboratory-of-genomics/.
Email: gsablok@ibch.poznan.pl
Prof. Luiza Handschuh
Email: luizahan@ibch.poznan.pl.
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Usage: ensemblcov <COMMAND>
Commands:
threaded-auto threaded version of ensembl auto gene conversion
auto-generate autogenerate the ensemble gene conversion
gtf-annotate-generate gtf file for annotation
countconvert id convert from counts file
differentialexpression id convert from differential expression
gene-ensembl gene list extraction from ensembl
exon-ensembl specific exons of the ensembl ids
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
- before running the ensemlcov additional options, run one time,either autogenerate or threaded-generate to link the ensemblid to geneid.
ensemblcov autogenerate yes
ensemblcov threaded-auto yes
ensemblcov countconvert ./sample-files/sample.matrix
ensemblcov differentialexpression ./sample-files/differntialresults.text
ensemblcov gtf-annotate-generate ./sample-files/sample.gtf
ensemblcov gene-ensembl id.txt
ensemblcov exon-ensembl ./sample-files/idexon.txt
- To install windows version:
rustup component add llvm-tools
rustup target add x86_64-pc-windows-msvc
git clone https://github.com/IBCHgenomic/ensemblcov.git
cd ensemblcov
cargo xwin build --target x86_64-pc-windows-msvc
- Acknowledgements: MOSAIC platform, developed as part of the ECBiG-MOSAIC project (POIR.04.02.00-00-D017/20), co-financed by the European Regional Development Fund (ERDF) under the Smart Growth Operational Programme 2014-2020, Measure 4.2 for the development of modern research infrastructure in the science sector.
- Project PI and Informal queries: Prof. Luiza Handschuh: luizahan@ibch.poznan.pl.
- Code related queries: Dr. Gaurav Sablok: gsablok@ibch.poznan.pl.
Gaurav Sablok Instytut Chemii Bioorganicznej Polskiej Akademii Nauk ul. Noskowskiego 12/14 | 61-704, Poznań Poland