Scientific Software
Updated 10 months ago

Pyrodigal — Peer-reviewed • Rank 15.6 • Science 100%

Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes - Published in JOSS (2022)

Scientific Software
Updated 10 months ago

Phylen — Peer-reviewed • Rank 2.2 • Science 95%

Phylen: automatic phylogenetic reconstruction using the EggNOG database - Published in JOSS (2018)

Scientific Software · Peer-reviewed
Updated 10 months ago

abyss • Rank 9.7 • Science 77%

:microscope: Assemble large genomes using short reads

Scientific Software
Updated 10 months ago

genomepy — Peer-reviewed • Rank 17.3 • Science 59%

genomepy: download genomes the easy way - Published in JOSS (2017)

Engineering (40%)
Scientific Software · Peer-reviewed
Updated 10 months ago

codonu • Rank 3.8 • Science 67%

A python project for analysis of codon usage for gene or genome analysis

Updated 10 months ago

karyoploteR • Rank 20.1 • Science 49%

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Updated 10 months ago

symbnet • Rank 2.6 • Science 59%

Teaching materials for SymbNET course: from MAGs to GEMs

Updated 10 months ago

genomeskim • Rank 1.6 • Science 57%

QC and filtering of genome skims, followed by organelle assembly and/or genome analysis

Updated 10 months ago

https://github.com/althonos/pyaragorn • Rank 7.4 • Science 49%

Cython bindings and Python interface to ARAGORN, a (t|mt|tm)RNA gene finder.

Updated 10 months ago

pyfastx • Rank 18.1 • Science 36%

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Scientific Software
Updated 10 months ago

LTRpred — Peer-reviewed • Rank 5.1 • Science 49%

LTRpred: de novo annotation of intact retrotransposons - Published in JOSS (2020)

Updated 10 months ago

valr • Rank 13.9 • Science 36%

Genome Interval Arithmetic in R

Updated 10 months ago

https://github.com/bernatgel/regioner • Rank 5.6 • Science 10%

An R/Bioconfuctor package for association analysis of genomic regions based on permutation tests

Updated 10 months ago

https://github.com/alexpreynolds/disjoint-windows • Rank 0.0 • Science 13%

Build a list of high-scoring, non-overlapping intervals using sampling or scheduling methods

Updated 10 months ago

genome_updater • Science 67%

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

Scientific Software
Updated 10 months ago

btllib — Peer-reviewed • Science 98%

btllib: A C++ library with Python interface for efficient genomic sequence processing - Published in JOSS (2022)

Updated 10 months ago

https://github.com/ay-lab/dchic • Science 23%

dcHiC: Differential compartment analysis for Hi-C datasets

Updated 10 months ago

catch • Science 75%

A package for designing compact and comprehensive capture probe sets.

Updated 10 months ago

sars-cov-2-sequenzdaten_aus_deutschland • Science 67%

Ein zentraler Bestandteil einer erfolgreichen Erregersurveillance ist das Verständnis der Verbreitung eines Erregers sowie seiner pathogenen Eigenschaften. Hierbei stellt das Wissen über das Erregergenom eine wichtige Informationsquelle dar. So erlaubt der Nachweis von Mutationen im Genom eines Erregers, Verwandtschaftsbeziehungen zu rekonstruie...

Updated 10 months ago

sammyseq • Science 67%

Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.

Updated 10 months ago

https://github.com/brentp/mosdepth • Science 26%

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Updated 10 months ago

references • Science 57%

nf-core/references is a bioinformatics pipeline that build references, for multiple use cases

Updated 10 months ago

mapsea • Science 57%

Mapping And Prediction of Shared Elements in Alignments

Updated 10 months ago

GenomAutomorphism • Science 46%

An R package to compute the autimorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group as described in the paper [Genomic Abelian Finite Groups](https://www.biorxiv.org/content/10.1101/2021.06.01.446543v2)

Updated 10 months ago

pyani-plus • Science 67%

Development repo for pyani-plus (the next iteration of pyani)

Updated 10 months ago

genepal • Science 57%

A Nextflow pipeline for genome and pan-genome annotation

Updated 10 months ago

ramen • Science 54%

Regional Association of Methylation variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify Variable Methylated Regions (VMRs) in microarray DNA methylation data. Additionally, using Genotype (G) and Environmental (E) data, it can identify which G, E, G+E or GxE model better explains this variability.

Updated 10 months ago

islandevolution.github.io • Science 44%

Source code for the Island biology, diversification, genome evolution lab