kullrich/scTEI

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kullrich/scTEI

kullrich

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add any phylogenetically based transcriptome evolutionary index (TEI) to single-cell data objects

snpless-nf

snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.

bio-scripts

collection of scripts for bioinformatic analysis

kakscalculator2

Fork of the KaKs_Calculator2.0 project https://sourceforge.net/projects/kakscalculator2

orthomap

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

MSA2dist

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

oggmap

oggmap is a python package to extract orthologous maps (short: orthomap or in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Oggmap results (gene ages per orthologous group) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

CRBHits

[CRBHits](https://github.com/kullrich/CRBHits) is a reimplementation of the Conditional Reciprocal Best Hit algorithm [crb-blast](https://github.com/cboursnell/crb-blast) in R.

EuroBioc2022_MSA2dist

Slide presentation and material for the software demo "Downstream Analysis of Synteny Networks with MSA2dist"

literal-dists

Convert a FASTA alignment with ambiguous nucleotides to literal distance matrix

dagchainer

Fork of the DAGchainer project https://sourceforge.net/projects/dagchainer

t2gGTF

extract transcript to gene table for DEG