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birthdeathmodel

Reciprocally retained genes in the angiosperm lineage show the hallmarks of dosage balance sensitivity

cross_species_annotation_transfer

Framework for transferring single-cell cluster annotations cross-species

i-adhore

i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.

igrn

iGRN data and code repository

ksrates

ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.

mini-ac

Motif-Informed Network Inference based on Accessible Chromatin (MINI-AC) is a method that combines accessible chromatin data from bulk or single-cell experiments with transcription factor binding site enrichment to learn gene regulatory networks in plants

mini-ex

Motif-Informed Network Inference of cell type-specific gene regulatory networks in plants

orthomclight

OrthoMCLight is an edited version of OrthoMCL v1.4 that requires less memory and has a faster runtime. It is a genome-scale algorithm for grouping orthologous protein sequences.

plantrrbs

Code base for RRBS and WGBS analyzes in Plants

tomato_motif_enrichment

trapid

TRAPID is a web application for the analysis of de novo transcriptomes

vhrr

vHRR: co-expression based gene function prediction