linsalrob
Professor of CS and Biology Writing bioinformatics code to study viruses, phages, and metagenomes.
Flinders UniversityAdelaide, Australia
Pinned Repositories
atavide
Atavistic processing of metagenomics data.
ComputationalGenomicsManual
Robs manual for the computational genomics and bioinformatics class.
EdwardsLab
Code from the Edwards lab, including bioinformatics, image analysis and more. All this code is created and maintained by folks at Rob Edwards' bioinformatics lab at Flinders University
fastq-pair
Match up paired end fastq files quickly and efficiently.
partie
PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE allows automatic separation of the data.
PhiSpy
Prediction of prophages from bacterial genomes
PhispyAnalysis
Analysis of phispy data
PyFBA
A python implementation of flux balance analysis to model microbial metabolism
sphae
Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!
SRA_Metadata
Get, parse, and extract information from the SRA metadata files
linsalrob's Repositories
linsalrob/SRA_Metadata
Get, parse, and extract information from the SRA metadata files
linsalrob/partie
PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE allows automatic separation of the data.
linsalrob/PyFBA
A python implementation of flux balance analysis to model microbial metabolism
linsalrob/ProphagePredictionComparisons
Comparisons of multiple different prophage predictions
linsalrob/PhageHosts
This is the complete code base used in Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, and Bas E. Dutilh (2015) Computational approaches to predict bacteriophage–host relationships. FEMS Microbiology Reviews doi: 10.1093/femsre/fuv048
linsalrob/mgi-adapters
Trim adapters from MGI sequence data
linsalrob/fasta_validator
C code to validate a fasta file
linsalrob/primer-trimming
Fast C code for identifying and removing primers and adapters
linsalrob/py_fasta_validator
A Python extension of the fasta validator
linsalrob/PhispyAnalysis
Analysis of phispy data
linsalrob/pyctv
Parse and incorporate the ICTV Virus Metadata Resource file
linsalrob/SearchSRA
Tools to search through the Sequence Read Archive using XSEDE's Jetstream
linsalrob/SearchSRAToolKit
Tools for processing data generated by the Search SRA
linsalrob/atavide
Atavistic processing of metagenomics data.
linsalrob/PHANOTATE
PHANOTATE: a tool to annotate phage genomes.
linsalrob/PPPF
Probabilistic Phage Protein Functions
linsalrob/adapter_benchmark
Benchmarking adapter and quality trimming tools
linsalrob/Bulk_RNAseq
Bulk RNA-seq & Differential Gene Expression Analysis Workshop Material
linsalrob/fastpath
A program to find the path through a network of nodes.
linsalrob/FOCUS
A model to identify organisms present in metagenomes in seconds
linsalrob/jetstream-search-sra
Search the SRA using the jetstream sra cluster setup
linsalrob/jetstream-search-sra-proteins
Use diamond to search the SRA
linsalrob/linsalrob.github.io
the linsalrob github.io pages
linsalrob/multiPhATE2
multiPhATE with comparative genomics
linsalrob/PhANNs
linsalrob/phcirc
Phage genome recircularization
linsalrob/Phicore
work in progress. but got to do with phage genomes because they are awesome!
linsalrob/prophage-distributions
Comprehensive analysis of Genbank prophage distributions
linsalrob/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
linsalrob/turbocor
Command line tool for computing gigantic correlation matrices