kullrich
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oggmap Public
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 ag…
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CRBHits Public
[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.
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bio-scripts Public
collection of scripts for bioinformatic analysis
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circlize Public
Forked from jokergoo/circlizeCircular visualization in R
R Other UpdatedFeb 16, 2025 -
syntenyPlotteR Public
Forked from Farre-lab/syntenyPlotteRR package to draw syntenic plots in 3 different styles
R Other UpdatedFeb 11, 2025 -
fastCN Public
Forked from KiddLab/fastCNPython GNU General Public License v3.0 UpdatedFeb 10, 2025 -
PolyPanner Public
Forked from eitanyaffe/PolyPannerLeveraging dense temporal sampling to improve assembly quality and identify high confidence polymorphic variants.
C++ GNU General Public License v3.0 UpdatedDec 5, 2024 -
TOFU-MAaPO Public
Forked from ikmb/TOFU-MAaPONextflow pipeline for the analysis of metagenomic short reads.
Nextflow GNU General Public License v3.0 UpdatedNov 29, 2024 -
bacterial-short-snake Public
Snakemake-powered commandline tool to do bacterial genome assembly, annotation and reference-based comparison using short-reads.
MIT License UpdatedNov 28, 2024 -
MSA2dist Public
MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
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vGWAS Public
Variance Heterogeneity Genome-wide Association Study - Reimplementation
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xenoseq Public
Forked from bramvandijk88/xenoseqPipeline to automate the comparison between short-read libraries to detect foreign ("xenotypic") sequences.
Shell GNU General Public License v3.0 UpdatedOct 10, 2024 -
carpentries-workshop-template Public template
Forked from carpentries/workshop-templateThe Carpentries Workshop Template
HTML Other UpdatedOct 9, 2024 -
dist2bionjs Public
Use stdin distance matrix to calculate bionjs
C++ GNU General Public License v2.0 UpdatedSep 24, 2024 -
awesome-pipeline Public
Forked from pditommaso/awesome-pipelineA curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
UpdatedSep 10, 2024 -
oggmapdb Public
A dashboard to explore and download orthomaps created with oggmap
MIT License UpdatedJul 31, 2024 -
bam2iupac Public
IUPAC FASTA extraction from BAM files to stdout
C++ MIT License UpdatedJun 24, 2024 -
literal-dists Public
Convert a FASTA alignment with ambiguous nucleotides to literal distance matrix
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OrthoFinder Public
Forked from davidemms/OrthoFinderPhylogenetic orthology inference for comparative genomics
Python GNU General Public License v3.0 UpdatedJun 1, 2024 -
TreeSwitchR Public
TreeSwitchR visualize phylogenetic trees along chromosomes in R
R Other UpdatedMay 14, 2024 -
snpless-nf Public
snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.
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minipileup Public
Forked from lh3/minipileupSimple pileup-based variant caller
C UpdatedMar 31, 2024 -
kortho Public
kortho calculates pairwise kmer jaccard distance between two peptide fasta files
GNU Affero General Public License v3.0 UpdatedMar 6, 2024 -
korthoCPP Public
korthoCPP calculates pairwise kmer jaccard distance between two peptide fasta files
C++ MIT License UpdatedMar 5, 2024 -
korthoR Public
korthoR calculates pairwise kmer jaccard distance between all sequences of an AAStringSet
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orthomap Public archive
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 orthogro…