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/dagchainer
Fork of the DAGchainer project https://sourceforge.net/projects/dagchainer
kullrich/EuroBioc2022_MSA2dist
Slide presentation and material for the software demo "Downstream Analysis of Synteny Networks with MSA2dist"
kullrich/orthologr
Genome wide orthology inference and dNdS estimation
kullrich/vGWAS
Variance Heterogeneity Genome-wide Association Study - Reimplementation
kullrich/breseq
breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R. More information at
kullrich/distSTRING
distSTRING calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
kullrich/funbiased
kullrich/Genes2Functions
This is a shiny app built around clusterProfiler to perform functional enrichment analysis from RNA-Seq DE analysis
kullrich/genome-grid
kullrich/genomeannotator
Pipeline for the identification of (coding) gene structures in draft genomes.
kullrich/kullrich.github.io
Personal website
kullrich/ltc_palettes
kullrich/myTAI
Evolutionary Transcriptomics with R
kullrich/protTrace
A simulation based framework to estimate the evolutionary traceability of protein.
kullrich/quickhla
kullrich/SAMap
SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.
kullrich/scikit-allel
A Python package for exploring and analysing genetic variation data
kullrich/snp-dists
Pairwise SNP distance matrix from a FASTA sequence alignment
kullrich/wtdbg2
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly