Repositories list

• deepclust-data

  Public
  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Sep 14, 2025Sep 14, 2025

• diamond

  Public
  Accelerated BLAST compatible local sequence aligner.

  C++

  •

  GNU General Public License v3.0

  •183•0•0•0•Updated Sep 14, 2025Sep 14, 2025

• deepclust_dataretrieval

  Public
  Cluster Extraction for the DeepClust Database

  Python

  •

  GNU General Public License v2.0

  •1•1•0•0•Updated Sep 12, 2025Sep 12, 2025

• orthologr

  Public
  Genome wide orthology inference and dNdS estimation

  blastcomparativer+ 17genomicsspeciescomparative-genomicsproteomeblast-searchesorthology-inferencecomparative-genomics-studies+ 10

  R

  •

  GNU General Public License v2.0

  •29•96•10•0•Updated Sep 5, 2025Sep 5, 2025

• myTAI

  Public
  Evolutionary Transcriptomics with R

  evolutiontranscriptomeevo-devo+ 9gene-setsrgene-expressionconservationevolutionary-transcriptomicsstudies-transcriptomesbiological-processes+ 2

  R

  •

  GNU General Public License v2.0

  •18•45•2•1•Updated Aug 29, 2025Aug 29, 2025

• evoGE

  Public
  Reproducible scripts for transcriptome evolution study

  R

  •2•0•0•0•Updated Jun 8, 2025Jun 8, 2025

• DevSeqPlant

  Public
  Web platform for plant evolutionary transcriptomics

  PHP

  •1•0•0•0•Updated Apr 16, 2025Apr 16, 2025

• philentropy

  Public
  Information Theory and Distance Quantification with R

  distance-measuresrstatistics+ 5information-theorysimilarity-measuresjensen-shannon-divergencedistance-quantificationparametric-distributions

  R

  •

  GNU General Public License v2.0

  •19•142•8•0•Updated Dec 5, 2024Dec 5, 2024

• setga

  Public
  Small library extracting a minimal subset from a given set that optimizes a given (set of) function(s).

  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 18, 2024Jul 18, 2024

• edgynode

  Public
  Statistical assessment and simulated evolution of gene regulatory networks

  R

  •

  GNU General Public License v3.0

  •3•4•0•0•Updated May 23, 2024May 23, 2024

• deepclust_colabfold

  Public
  Using the DeepClust Database with ColabFold

  Python

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Apr 11, 2024Apr 11, 2024

• uberblast

  Public
  Seamless Integration of BLAST Alignments in R

  GNU General Public License v2.0

  •1•0•0•0•Updated Oct 28, 2023Oct 28, 2023

• rdiamond

  Public
  Running DIAMOND2 through R

  diamondsequencesequence-alignment+ 1aligner

  R

  •

  GNU General Public License v2.0

  •2•7•0•0•Updated Oct 17, 2023Oct 17, 2023

• published_phylomaps

  Public
  A Collection of Published Phylostratigraphic Maps and Divergence Maps

  3•10•1•0•Updated Oct 12, 2023Oct 12, 2023

• metablastr

  Public
  Seamless Integration of BLAST Sequence Searches in R

  proteinspeciesblast+ 9blast-searchesnucleotidebiological-sequencesblastingblastnblast-searchsequence-diversity+ 2

  R

  •

  GNU General Public License v2.0

  •6•30•6•1•Updated Sep 10, 2023Sep 10, 2023

• LTRpred

  Public
  De novo annotation of young retrotransposons

  pipelinegenomeevolution+ 4ltrdiversificationltr-transposonsltr-retrotransposons

  R

  •

  GNU General Public License v2.0

  •9•48•5•0•Updated Apr 12, 2022Apr 12, 2022

• retrocombinator

  Public
  An R/C++ package for simulating the evolution of retrotransposons over time.

  evolutiontranspositionspeciation+ 4transposonsrecombinationretrotransposonstransposable-element

  HTML

  •3•4•1•0•Updated Apr 1, 2022Apr 1, 2022

• network-inference-pipeline

  Public
  Applying network-inference-toolbox to RNAseq data

  R

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Nov 3, 2021Nov 3, 2021

• network-inference-toolbox

  Public
  A bunch of network inference utilities packaged as Singularity containers

  R

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Apr 22, 2021Apr 22, 2021

• homologr

  Public
  Homology inference across multiple species

  R

  •0•1•0•0•Updated Sep 27, 2020Sep 27, 2020

• seqstats

  Public
  Biological Sequence Statistics in R

  bioinformaticsgenomicsbiological-data-analysis+ 2biological-sequencesbiological-sequence-statistics

  R

  •1•2•0•0•Updated Apr 26, 2020Apr 26, 2020

• patternseqr

  Public
  Sequence feature detection and classification with R

  R

  •0•1•0•0•Updated Apr 22, 2020Apr 22, 2020

• biodbretrievr

  Public
  Retrieve and efficiently index entire biological sequence databases

  dataretrievalbiological-sequences+ 2biological-datadatabasestoring

  0•0•0•0•Updated Apr 21, 2020Apr 21, 2020

• shinyDIAMOND

  Public
  A web interface to DIAMOND2

  0•0•0•0•Updated Apr 18, 2020Apr 18, 2020

• biomartr

  Public
  Genomic Data Retrieval with R

  R

  •29•0•0•0•Updated Apr 12, 2020Apr 12, 2020

• hitparsr

  Public
  Distributed Databasing of Alignment Hit Data

  distributed-databasedistributed-storagedistributed-file-system

  0•0•0•0•Updated Apr 7, 2020Apr 7, 2020