Pinned Repositories
AEGeAn
Integrated toolkit for analysis and evaluation of annotated genomes
bghandbook
Handbook for Brendel Group students, postdocs, and staff
BWASP
Bisulfite-seq data Workflow Automation Software and Protocols
GoSTRIPES
Computational workflows for STRIPE-seq data analyses
MoVRs
Motif set Reduction and Validation (MoVRs) - a workflow for the derivation of genome-wide DNA motif detection and vetting
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
Brendel Group's Repositories
BrendelGroup/AEGeAn
Integrated toolkit for analysis and evaluation of annotated genomes
BrendelGroup/SRAssembler
Selective and Recursive local Assembler
BrendelGroup/MoVRs
Motif set Reduction and Validation (MoVRs) - a workflow for the derivation of genome-wide DNA motif detection and vetting
BrendelGroup/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
BrendelGroup/bghandbook
Handbook for Brendel Group students, postdocs, and staff
BrendelGroup/GoSTRIPES
Computational workflows for STRIPE-seq data analyses
BrendelGroup/FMAB
Fundamental Models and Algorithms in Bioinformatics
BrendelGroup/TRegGA
Targeted reference-guided genome assembly for comparative rice genomics
BrendelGroup/BWASP
Bisulfite-seq data Workflow Automation Software and Protocols
BrendelGroup/bgSingularityHub
A portal to our collection of Singularity/Apptainer definition and image files
BrendelGroup/BWASPR
R functions and scripts to process output from the BWASP workflow
BrendelGroup/code4Rice3K
code developed for the analysis of the Rice 3000 Genomes project data
BrendelGroup/GeneSeqer
Sensitive spliced-alignment of cDNAs or proteins
BrendelGroup/GoRAMPAGE
GoRAMPAGE - a workflow for promoter detection by 5'-read mapping
BrendelGroup/HymHub
HymHub is now GenHub
BrendelGroup/TSRchitect
Promoter identification from diverse types of large-scale TSS profiling data
BrendelGroup/IntervalLoci
Supplemental documentation for the iLocus paper
BrendelGroup/TSRbuild
Scripts and workflows for transcription start region (TSR) exploration
BrendelGroup/xGDBvm
Code for the xGDBvm iPlant Atmosphere enabled genome annotation platform
BrendelGroup/AllRice
Code for rice genome analyses (but not necessarily only rice)
BrendelGroup/Bismark
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
BrendelGroup/brendelgroup.github.io
Brendel Group - github.io presence
BrendelGroup/CTBPprj
BrendelGroup/GAinSAW
Workflows for genome alignment chain file selection and annotation tasks
BrendelGroup/iLoci_SLB22NARGB
Procedures and data for the iLoci study described in Standage, Lai and Brendel (2022)
BrendelGroup/mRNAmarkup
Evaluation and annotation of assembled transcripts
BrendelGroup/PRDM16_CtBP_Project
Workflows and documentation for Baizabal Group genomics projects on neural stem cells