Jason Stajich Lab at UC Riverside

Login: stajichlab

Company: null

Location: RIverside, CA

email: stajichlab@stajich.org

Blog: http://lab.stajich.org

Members

1. Jason Stajich

Repositories

A_fumigatus_popgen

Population genetics for A.fumigatus

Afum_popgenome

Popgenomics for Aspergillus fumigatus

ahrendt_thesis

Steven Ahrendt thesis

antarctic-genomes

Antarctica genome assembly & genomes

batrachochytrium

Archived files from previous publication data

BdHp_RNASeq

RNASeq analysis of Bd and Hp strains

bd_popgen

Population genomics analysis of Bd

Bioinformatics-Training

Bioinformatics training resources

Candida_lusitaniae

Candida lusitaniae population genomics

Candida_phosphoproteome

Candida albicans phosphoproteome

Cauris_popgenomics

Candida auris population genomics analyses

cellwall_family_pipeline

cell wall gene family identification pipeline

Chaetomium_Neurospora

Chaetomium Neurospora comparison

Chaetosphaeria

null

chytropsin

Chytridopsin identification and phylogenetic project

C_lusitaniae_DHED1_RNAseq

C. lusitaniae DHED1 run 1

C_lusitaniae_popseq

Genomic analyses of Clavispora (Candida) lusitaniae strains

Comparative_pipeline

Comparative genomics pipeline

coprinopsis_PNAS_2010

Coprinopsis genome paper 2010

DAP

Plant M18 aspartyl aminopeptidases (DAP) paper

FGMP

Fungal Genome Mapping Pipeline

FUNGuild

FUNGuild: parsing OTUs into functional guilds

GAG_cluster

Analysis of GAG cluster

GCI

gene conservation index

general-genomics-tools

General purpose tools for genomics tools for the lab used in publications.

GenoAnnoFlow

Genome annotation pipeline and Visualization

GenomeAnnotation

Description of Genome Annotation Procedures

H3K27

H3K27 neurospora project

HeatMapExplorer

Heat Map Exploring Java tool

HMM_profile_genomes

using hmmer, count copies of an HMM in proteomes, cut out the copies, and build trees from these, build heatmaps and tables

Hortaea_werneckii

Hortea experimental evolution and reannotation project

labmeeting-snippets

Lab meeting code review and examples

localizaTE

de novo and homology based Transposable Element annotation system

Microbiome_Coprophilome_ElkDung

Elk Dung Coprophilome via JGI-CSP

Microbiome_resources

Microbiome tools and resources for Stajichlab projects

mTEA

Mosquito TE Annotation

Nanopore_Lambda2016-10-12

Lambda nanpore run

neolecta

neolecta annotation and analysis

neurospora_MSUD

Neurospora MSUD project

OrthoMCL

null

Phyling

Phylogenomics pipeline for extracting a conserved marker set from unassembled sequencing reads

PHYling_unified

Unified PHYling pipeline for annotated genomes and unassembled datase

popCNV

Population level CNV investigation tools from resequencing data

RelocaTE

Find the locations of TEs using the TSD in unassembled short reads by comparing to a closely related reference genome assembly

RelocaTE2

This tool is for mapping TEs from resequencing data: Stajich lab

REPET-slurm

SLURM-ready bash scripts to run the complete REPET pipeline

riceBS

Rice Bisulfide sequencing support

RNASeq_tutorial

Tutorial on RNASeq

rozella

Rozella genome project

Rstol_popgenomics

Rhizopus stolonifer population genomics

rumen_meta

Rumen Metatranscriptome project

SPB_Centriole_Flagella

Analyses of proteins defined as Centriole, Flagellum, or Spindle-pole body from literature

TARGeT

Tree Analysis of Related Genes and Transposons

Test_LabMeeting

This is a test for lab

Westberg_DataDownload

Download Sequences from GenBank based on a datafile

Zygo_MucoralesVirulence

Virulence factors conservation profiling