zongzhiwu Goto Github PK

basalt

busco-mag-phylogeny

Construction of concatenated gene tree from BUSCO genes

cenote-taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs

demovir

Taxonomic classification of viruses at Order and Family level

emg-viral-pipeline

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

ggcor

Extended tools for correlation analysis and visualization.

gggenes

➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

gggenomes

A grammar of graphics for comparative genomics

ggmap

A package for plotting maps in R with ggplot2

glimps

A User-Friendly Pipeline for the production of Core Genome and Concatenated Protein based Phylogenetic Trees and Protein based Comparative Genomic Analyses

gtdbtk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

gwvc

Custom codes for the Groundwater Virome Database (GWVD)

marker-genes-as-predictors-of-shared-genomic-function

Scripts and data for Sevigny et al. 2018. Marker genes as predictors of shared genomic function.

mattolm-public-scripts

Scripts in support of publication

metagenome_analyses

Using IDBA-ud, this is how we assemble metagenomic reads into scaffolds on different projects

metapop

A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations

mgv

Supporting code for uncultivated gut virus manuscript

mlst

Short python script designed to identify housekeeping genes in protein files, concatenate them, and create a MLST phylogeny

multiphate2

multiPhATE with comparative genomics

my_bioinformatics

ncbitax2lin

🐞 Convert NCBI taxonomy dump into lineages

ogfilter

A script that parses the OrthoFinder output and keeps only the orthogroups that meet specific criteria

orthocounts2bin

A script to get from Orthogroups.GeneCount.tsv to a gene presence/absence binary alignment.

phylorank

Assign taxonomic ranks based on evolutionary divergence.

pkuautosubmit-action

百京大学燕园云战役自动填报小助手 Github Action

plasmapr

Creating plasmid maps inside ggplot.

rna2virus

Pipline for detecting viral sequences from RNA-seq data

useful_scripts

vgea

VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.

vhulk

viral Host UnveiLing Kit (vHULK)