Genomic Open-source Breeding informatics initiative
To build open-source genomic data management and analysis tools to enable breeders to implement genomic and marker-assisted selection as part of their routine breeding programs. To transform b...1276 days ago
Breedbase is a comprehensive breeding management and analysis software
Breedbase is a comprehensive breeding management and analysis software. It can be used to design field layouts, collect phenotypic information using tablets, support the collection of genotyping...1276 days ago
Calling variants in non-diploid systems
The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true...1105 days ago
QuasR: Quantification and annotation of short reads in R
The QuasR package (short for Quantify and annotate short re...at2 package). The package aims to cover the whole analysis workflow of typical high thro...ngle R script can contain all steps of a complete analysis, making it simple to document...1057 days ago
Kmer: a suite of tools for DNA sequence analysis
More at https://help.rc.ufl.edu/doc/Kmer This also includes: A2Amapper: ATAC,...In addition to providing random access to the base level, it includes several analysis functions. Meryl:...1053 days ago
RNA-Seq differential expression work flow using DESeq2
One of the aim of RNAseq data analysis is the detection of differentially expressed genes. The package DESeq2 provides methods to test for differential expression analysis.1047 days ago
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RNA-seq workflow: gene-level exploratory analysis and differential expression
Here we walk through an end-to-end gene-level RNA-seq differential expressio...transcripts, and prepare gene-level count datasets for downstream analysis. We will perform exploratory data analysis (EDA) for quality assessment...1000 days ago
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