stephenda Goto Github PK

advancedheatmaptutorial

for YouTube Channel

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

breakdancer

SV detection from paired end reads mapping

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

cgview_comparison_tool

The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.

code_snippets

dash

Analytical Web Apps for Python, R, Julia, and Jupyter. No JavaScript Required.

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

dfast_core

DDBJ Fast Annotation and Submission Tool

difflinker

DiffLinker: Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design

dotfiles

My dotfiles and personal preferences

figtree

Automatically exported from code.google.com/p/figtree

flowers

R package for generating flower plots

fripan

Interactive, web tool for exploring pan-genome of bacterial strains

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

hmmer

HMMER: biological sequence analysis using profile HMMs

koala-formatter

Script for converting raw KO-number output from GhostKOALA and BlastKOALA into hierarchically-structured CSV format

mesquitecore

The core Mesquite repository

mlstar

An easy way of MLSTyping your genomes in R.

msu_ngs2015

DE analysis module for Week3

mummer

Mummer alignment tool

nested-pie-chart

Nested Pie Chart in MatPlotLib for your dataset

networkd3

D3 JavaScript Network Graphs from R

new-git-test

orthofinder

Phylogenetic orthology inference for comparative genomics

orthologr

Genome wide orthology inference and dNdS estimation

pca_demo

phylogenetics

Phylogenetic analyses code

phytools

plotly-tutorial

This Jupyter Notebook condenses the Plotly API into one easy to use document with examples