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analysis-of-species-transcriptome-wgcna

WGCNA analysis was conducted to integrate different data from different articles of the same species to find the defense modules of each species

book

clusterprofiler

:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters

de-wrapper-scripts

Perl scripts used to wrap application published in the DE

findgse

findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a skew normal distribution model.

gce

GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size ,genomic repeat content and the heterozygsis rate of the sequencing sample.

googlr

Googlr is a command line tool that lets you search Google from your terminal.

grn

Maize Gene regulatory network (MaizeGRN)

ilpbdb

isoseq

IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

jcvi

Python library to facilitate genome assembly, annotation and comparative genomics

learn-bioinformatics

maize_tissue-specific_grn

The repository source code for maize tissue-specific GRN project

nextdenovo

Fast and accurate de novo assembler for third generation sequencing (TGS) reads

onekp-gene-family-evo

Gene family evolution analysis of OneKP capstone paper

orthofinder

Phylogenetic orthology inference for comparative genomics

rnaseq

public RNA-Seq datasets

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rnaseq_workflow

snakemake workflow for bulk RNA-seq workflow using STAR-edgeR

roary

Rapid large-scale prokaryote pan genome analysis

snakemake-rnaseq-workflow

Snakemake Pipeline for RNASeq Workflow

to-gcn

Pipeline of time-ordered gene coexpression network (TO-GCN) construction from three-dimensional (gene expression, condition, and time) data

webscst

A web tool for single-cell RNA-seq data and spatial transcriptome data integration

webservice-clients

A collection of Web Service Clients to consume EBI's tools via REST and SOAP APIs.