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atlas

RNA-Seq and Proteomic Atlas of Maize Development

grn

Maize Gene regulatory network (MaizeGRN)

IntegrativeNetworkMap

STRling

Detect novel (and reference) STR expansions from short-read data

SolEvo_PotatoDele

Use hifi to assembly the Sol genome, and dissecting Sol evo

TOGA

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Age_Structure

Copy of Jianing's repo

RCrashCourse_Book

A GitBook version of the R Crash Course self-tutorials: https://colauttilab.github.io/RCrashCourse

panpop

Application of pan-genome for population

srf

SRF: Satellite Repeat Finder

m6anet

Detection of m6A from direct RNA-Seq data

designer

Prototype UI for Shiny Apps

MaizeHeatStress

ggplot_tricks

Here, I collect some tricks I've learned about the {ggplot2} R package

training-collection

Collection of bioinformatics training materials

psvcp_v1.01

Pan-genome Construction and Population Structure Variation Calling pipeline

plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.

MCHelper

MCHelper: An automatic tool to curate transposable element libraries

vcf2hmp

convert VCF to HMP format

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

bioinformatics

:microscope: Path to a free self-taught education in Bioinformatics!

assertr

Assertive programming for R analysis pipelines

BatMeth2

BS-seq analysis pipeline

ggview

Ggplot picture previewer

slider

Sliding Window Functions

GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

aRt

R package to create generative art.

basegraphics

Pretty plots using pure base graphics in R

tidybulk

Brings bulk and pseudobulk transcriptomics to the tidyverse

wgap

Whole Genome Annotation Pipeline