michaelgruenstaeudl
Assistant Professor, Fort Hays State University
Fort Hays State UniversityHays, Kansas
Pinned Repositories
airpg
Accessing the inverted repeats of archived plastid genomes
airpg_newFeatures
New features for airpg
annonex2embl
Converts an annotated DNA multi-sequence alignment (in NEXUS format) to an EMBL flatfile for submission to ENA
BEAUTiAutomator
A Python script that automates the generation of the XML input files of BEAST (Drummond et al. 2012) and *BEAST (Heled & Drummond 2010)
Bioinf-Example__RNA-seq_mapping_and_count_target_gene
Bioinformatics example: Mapping RNA seq data and inferring count for gene of interest
Botany2021_Workshop
Workshop W14 during the conference Botany 2021
full-text-literature-mining-on-pubmed
Full text literature mining on PubMed for keyword combinations
PACVr
Plastome Assembly Coverage Visualization in R
StandardizedPlastidPhylogenomics
Pipeline to automate and standardize the bioinformatic processes in plastid phylogenomics
WARACS
WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States
michaelgruenstaeudl's Repositories
michaelgruenstaeudl/airpg
Accessing the inverted repeats of archived plastid genomes
michaelgruenstaeudl/PACVr
Plastome Assembly Coverage Visualization in R
michaelgruenstaeudl/Botany2021_Workshop
Workshop W14 during the conference Botany 2021
michaelgruenstaeudl/full-text-literature-mining-on-pubmed
Full text literature mining on PubMed for keyword combinations
michaelgruenstaeudl/StandardizedPlastidPhylogenomics
Pipeline to automate and standardize the bioinformatic processes in plastid phylogenomics
michaelgruenstaeudl/WARACS
WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States
michaelgruenstaeudl/airpg_newFeatures
New features for airpg
michaelgruenstaeudl/annonex2embl
Converts an annotated DNA multi-sequence alignment (in NEXUS format) to an EMBL flatfile for submission to ENA
michaelgruenstaeudl/BEAUTiAutomator
A Python script that automates the generation of the XML input files of BEAST (Drummond et al. 2012) and *BEAST (Heled & Drummond 2010)
michaelgruenstaeudl/Bioinf-Example__RNA-seq_mapping_and_count_target_gene
Bioinformatics example: Mapping RNA seq data and inferring count for gene of interest
michaelgruenstaeudl/Bioinformatics_course__Fall2023
Some coding exercises of the bioinformatics course I am teaching in fall 2023
michaelgruenstaeudl/CNN_monocot_dicot_rootXS
Image classification for differentiating dicot and monocot root cross sections using a convolutional neural network
michaelgruenstaeudl/CommT_Code
R code for the Community Tree project
michaelgruenstaeudl/CommTViz
R visualizations for the Community Tree project
michaelgruenstaeudl/consel_MPI
CONSEL: for assessing the confidence of phylogenetic tree selection - MPI version
michaelgruenstaeudl/cpGenomeCorrector
Facilitating submission and updates of plastid genomes on NCBI
michaelgruenstaeudl/EEOB563-Spring2023
Practical phylogenetics course
michaelgruenstaeudl/EMBL2checklists
Converts EMBL-formatted flatfiles to ENA checklists for submission via the interactive Webin submission system
michaelgruenstaeudl/FAAUTeC
Continuation of development of FAAUTeC
michaelgruenstaeudl/GoncalvesEtAl2019_Analyses
Code used in the analyses of Gonçalves et al. (2019)
michaelgruenstaeudl/HybridLambdaTools
Helper tools for the software package Hybrid-Lambda (Zhu et al. 2013, arXiv:1303.0673)
michaelgruenstaeudl/P2C2M_Code
R code of P2C2M
michaelgruenstaeudl/P2C2M_Visualizations
Visualizations for scientific publication of P2C2M (Gruenstaeudl et al. 2015)
michaelgruenstaeudl/partitionedNex2MrBayes
Shell scrip to convert a partitioned NEXUS file to input for the phylogeny inference software MrBayes
michaelgruenstaeudl/PlastomeBurstAndAlign
A Python tool to extract and align genes, introns, and intergenic spacers across hundreds of plastid genomes using associative arrays
michaelgruenstaeudl/PlastomeCoverageDepthEvenness
Continuation of the development of the pipeline to evaluate the depth and evenness of plastome sequence coverages
michaelgruenstaeudl/SnakemakePlastidPhylogenomics
Snakemake workflow for StandardizedPlastidPhylogenomics
michaelgruenstaeudl/starter-hugo-academic