Pinned Repositories
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
BWASP
Bisulfite-seq data Workflow Automation Software and Protocols
CodeFMAB
code and supplementary documents supporting the FMAB book project
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
TSRbuild
Scripts and workflows for transcription start region (TSR) exploration
TSRchitect
Promoter identification from large-scale TSS data
vpbrendel's Repositories
vpbrendel/CodeFMAB
code and supplementary documents supporting the FMAB book project
vpbrendel/MoVRs
Motif set Reduction and Validation (MoVRs) - a workflow for the derivation of genome-wide DNA motif detection and vetting
vpbrendel/AEGeAn
Integrated toolkit for analysis and evaluation of annotated genomes
vpbrendel/AllRice
Code for rice genome analyses (but not necessarily only rice)
vpbrendel/bghandbook
Handbook for Brendel Group students, postdocs, and staff
vpbrendel/bgSingularityHub
A portal to our collection of Singularity/Apptainer definition and image files
vpbrendel/BWASP
Bisulfite-seq data Workflow Automation Software and Protocols
vpbrendel/GoSTRIPES
Computational workflows for STRIPE-seq data analyses
vpbrendel/TSRbuild
Scripts and workflows for transcription start region (TSR) exploration
vpbrendel/TSRchitect
Promoter identification from large-scale TSS data
vpbrendel/Bioinformatics-Lab-GitHub-Demo
vpbrendel/Bismark
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
vpbrendel/bsmap
vpbrendel/BWASPR
R functions and scripts to process output from the BWASP workflow
vpbrendel/CAGEfightR
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
vpbrendel/code4Rice3K
code developed for the analysis of the Rice 3000 Genomes project data
vpbrendel/CTBPprj
Fork of BrendelGroup/CTBPprj
vpbrendel/DSBS
vpbrendel/GAinSAW
Workflows for genome alignment chain file selection and annotation tasks
vpbrendel/GeneSeqer
Sensitive spliced-alignment of cDNAs or proteins
vpbrendel/genhub
Explore eukaryotic genome composition and organization with iLoci
vpbrendel/GoRAMPAGE
GoRAMPAGE - a workflow for promoter detection by 5'-read mapping
vpbrendel/iLoci_Lai2020
Procedures and data for the iLoci study described in Lai et al. (2020)
vpbrendel/iLoci_SLB22NARGB
Procedures and data for the iLoci study described in Standage, Lai and Brendel (2022)
vpbrendel/mrbo-tn
This is an implementation of modified RBO in the case of ranking gene lists.
vpbrendel/mRNAmarkup
Evaluation and annotation of assembled transcripts
vpbrendel/SRAssembler
Selective and Recursive local Assembler
vpbrendel/TMPbgSingularityHub
A portal to our collection of singularity definition and image files
vpbrendel/TSRexploreR
vpbrendel/VMutil
some useful instructions and files to get me going on newly launched VMs