Overview of Bioinformatic Resources

Introduction

the bioinfo repository contains a collection of tools and resources for bioinformatic data processing and manipulation. at present, the majority of these focus on processing single cell transcriptomics:

• manipulating genomic annotations (from gff/gtf3 files). building annotation indices, filtering, id-conversion and statistics about gene lengths and exon lengths (which may be of use when normalizing non-UMI based data)
• genome sequence mapping (star and cell ranger) scripts and indices.
• handling single cell protocols (configuration of umis, etc.)
• handling raw sequence reads (fastq file operations)
• procedures after generating an expression matrix. assigning sample metadata, mapping the cell ranger (or star) result to a specified gff file. basic quality controls (including doublet detection), normalization (including sequence length correction for non-UMI dataset, log normalization, sctransform, harmony, scvi etc.). data scaling. integration of multiple experiments. dimension reduction (pca, umap and tsne, with plotting). clustering. differential expression. gene set enrichment. pseudo-time analyses (monocle). and intercellular ligand-receptor interactions (cpdb).

Notes

• all the listed works are under an open license (either GPL, MIT or CC-BY).
• any questions or suggestions, please write to xornent at outlook dot com

Last updated: Sept. 2024