Plant Bioinformatics

Using GenBank and SRA.- Scripting Analyses of Genomes in Ensembl Plants.- CyVerse for Reproducible Research: RNA-Seq Analysis.- Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources.- Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.- CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource.- The Barley and Wheat Pan-Genomes.- Basics of Bash.- Pipeline Automation via Snakemake.- SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data.- Trimming and Validation of Illumina Short Reads Using Trimmomatic, Trinity Assembly, and Assessment of RNA-Seq Data.- De Novo Assembly of Linked Reads Using Supernova 2.0.- Applications of Optical Mapping for Plant Genome Assembly and Structural Variation Detection.- Making a Pangenome Using the Iterative Mapping Approach.- Construction of Practical Haplotype Graph (PHG) with the Whole Genome Sequence Data.- Visualization Tools for Genomic Conservation.- Annotation of Protein-Coding Genes in Plant Genomes.- Finding and Characterizing Repeats in Plant Genomes.- Gene Co-Expression Network Analysis.- Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies.- Managing High-Density Genotyping Data with Gigwa.- Machine Learning for Image Analysis: Leaf Disease Segmentation.- Analysis of Bisulphite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions.- Long Intergenic Non-Coding RNA (lincRNA) Discovery from Non-Strand Specific RNA-Seq Data.- Linkage Disequilibrium Statistics and Block Visualization.- Analysis of Small RNA Sequencing Data in Plants.- Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases.- AgroLD: A Knowledge Graph Database for Plant Functional Genomics.