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assemblage

Tools for working with second gen assemblies, fasta sequences, etc

cpp-0-1-resource

C++ 匠心之作 从0到1入门资料

easymicrobiome

Scripts and databases for amplicon and metagenome

evee-tools

EVEE-Tools is a suite of scripts for analyzing expression evolution across species.

expressionml

forwardgenomics

Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework

geo

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science

interspecific_rnaseq

killigenomics

Killifish genomics scripts

learnnote

Bioinformatics

liu-wq.github.io

maker-genome-annotations-tutorial

Construct ab initio gene prediction using only BUSCO augustus models. Add in transcriptome for extra support

methylation_analysis

Learn methylation

mixr

MIXR: Mismatching Isoform eXon Remover

polysel

Pipeline to detect polygenic selection in gene sets

ratite-genomics

Scripts and other material for the assembly and analysis of ratite genomes.

reg_evo_primates

This is a GitHub repo for a project studying gene expression and methylation in humans, chimpanzees, and rhesus macaques. The website of this work can be found at:

regulatory_evol

The website with the results can be found at https://lauren-blake.github.io/Regulatory_Evol/analysis/

rna-seq-diff-exprn

RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).