github.com - identify potential contaminants or horizontally transferred genes in transcriptomes.
algorithm is based on alogorithm described in the following: Gladyshev, Eugene A., Matthew Meselson, and Irina R. Arkhipova. "Massive horizontal gene transfer in...
github.com - For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aidenlab.org/assembly.
For the original version of the pipeline and to reproduce the...
github.com - Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables painless integration with the TensorFlow machine learning framework,...
www.oreilly.com - BioCoder features:
Novel therapeutic discovery strategies
Hardware such as low-cost lab equipment or diagnostics
Open or low-cost bioinformatics tools
Engineered organisms for the production of small molecules, biologics, or other...
github.com - AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies
SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for...
colab.research.google.com - You can: improve your Python programming language coding skills. develop deep learning applications using popular libraries such as Keras, TensorFlow, PyTorch, and OpenCV.
If you have just a single notebook to submit, use the...
https://www.raku.org/ - Raku is a member of the Perl family of programming languages. Formerly known as Perl 6, it was renamed in October 2019. Raku introduces elements of many modern and historical languages. Compatibility with Perl was not a goal, though a compatibility...
http://efs.heiderlab.de/ - The software EFS (Ensemble Feature Selection) makes use of multiple feature selection methods and combines their normalized outputs to a quantitative ensemble importance. Currently, eight different feature selection methods have been integrated in...
github.com - genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms
More at https://github.com/ekg/mutatrix
./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta
github.com - glia's main use is as a local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM alignments.
More at https://github.com/ekg/glia
glia -f...