Pinned Repositories
bio-scripts
collection of scripts for bioinformatic analysis
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.
dagchainer
Fork of the DAGchainer project https://sourceforge.net/projects/dagchainer
kakscalculator2
Fork of the KaKs_Calculator2.0 project https://sourceforge.net/projects/kakscalculator2
korthoR
korthoR calculates pairwise kmer jaccard distance between all sequences of an AAStringSet
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.
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.
scTEI
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.
kullrich's Repositories
kullrich/snpless-nf
snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.
kullrich/bio-scripts
collection of scripts for bioinformatic analysis
kullrich/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.
kullrich/MSA2dist
MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
kullrich/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.
kullrich/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.
kullrich/korthoR
korthoR calculates pairwise kmer jaccard distance between all sequences of an AAStringSet
kullrich/literal-dists
Convert a FASTA alignment with ambiguous nucleotides to literal distance matrix
kullrich/vGWAS
Variance Heterogeneity Genome-wide Association Study - Reimplementation
kullrich/angsd
Program for analysing NGS data.
kullrich/awesome-pipeline
A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
kullrich/bacterial-short-snake
Snakemake-powered commandline tool to do bacterial genome assembly, annotation and reference-based comparison using short-reads.
kullrich/bam2iupac
IUPAC FASTA extraction from BAM files to stdout
kullrich/bioconda-recipes
Conda recipes for the bioconda channel.
kullrich/carpentries-workshop-template
The Carpentries Workshop Template
kullrich/dist2bionjs
Use stdin distance matrix to calculate bionjs
kullrich/introgression
kullrich/kortho
kortho calculates pairwise kmer jaccard distance between two peptide fasta files
kullrich/korthoCPP
korthoCPP calculates pairwise kmer jaccard distance between two peptide fasta files
kullrich/lordec-miniasm
kullrich/minipileup
Simple pileup-based variant caller
kullrich/oggmapdb
A dashboard to explore and download orthomaps created with oggmap
kullrich/OrthoFinder
Phylogenetic orthology inference for comparative genomics
kullrich/PolyPanner
Leveraging dense temporal sampling to improve assembly quality and identify high confidence polymorphic variants.
kullrich/published_phylomaps
A Collection of Published Phylostratigraphic Maps and Divergence Maps
kullrich/syntenet
An R package to infer and analyze synteny networks from protein sequences
kullrich/syntenyPlotteR
R package to draw syntenic plots in 3 different styles
kullrich/TOFU-MAaPO
Nextflow pipeline for the analysis of metagenomic short reads.
kullrich/TreeSwitchR
TreeSwitchR visualize phylogenetic trees along chromosomes in R
kullrich/xenoseq
Pipeline to automate the comparison between short-read libraries to detect foreign ("xenotypic") sequences.