brendelgroup Goto Github PK

aegean

Integrated toolkit for analysis and evaluation of annotated genomes

allrice

Code for rice genome analyses (but not necessarily only rice)

bghandbook

Handbook for Brendel Group students, postdocs, and staff

bgsingularityhub

A portal to our collection of Singularity/Apptainer definition and image files

bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

brendelgroup.github.io

Brendel Group - github.io presence

bwasp

Bisulfite-seq data Workflow Automation Software and Protocols

bwaspr

R functions and scripts to process output from the BWASP workflow

code4rice3k

code developed for the analysis of the Rice 3000 Genomes project data

ctbpprj

fmab

Fundamental Models and Algorithms in Bioinformatics

gainsaw

Workflows for genome alignment chain file selection and annotation tasks

geneseqer

Sensitive spliced-alignment of cDNAs or proteins

gorampage

GoRAMPAGE - a workflow for promoter detection by 5'-read mapping

gostripes

Computational workflows for STRIPE-seq data analyses

hymhub

HymHub is now GenHub

iloci_slb22nargb

Procedures and data for the iLoci study described in Standage, Lai and Brendel (2022)

intervalloci

Supplemental documentation for the iLocus paper

movrs

Motif set Reduction and Validation (MoVRs) - a workflow for the derivation of genome-wide DNA motif detection and vetting

mrnamarkup

Evaluation and annotation of assembled transcripts

pdom-genome-project

Polistes dominula genome project, a collaboration between the Insect Sociogenomics Lab at Iowa State University and the Computational Genome Science Lab at Indiana University

srassembler

Selective and Recursive local Assembler

tregga

Targeted reference-guided genome assembly for comparative rice genomics

tsrbuild

Scripts and workflows for transcription start region (TSR) exploration

tsrchitect

Promoter identification from diverse types of large-scale TSS profiling data

xgdbvm

Code for the xGDBvm iPlant Atmosphere enabled genome annotation platform