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.
Language:Python2 4 72
ComputationalGenomicsManual
Robs manual for the computational genomics and bioinformatics class.
Language:HTML230 11 161
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
Language:Jupyter Notebook39 9 116
fastq-pair
Match up paired end fastq files quickly and efficiently.
Language:C144 5 2232
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.
Language:Perl25 7 46
PhiSpy
Prediction of prophages from bacterial genomes
Language:Jupyter Notebook73 10 5521
PhispyAnalysis
Analysis of phispy data
Language:Jupyter Notebook4 5 02
PyFBA
A python implementation of flux balance analysis to model microbial metabolism
Language:Python26 6 914
sphae
Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!
Language:Python28 5 139
SRA_Metadata
Get, parse, and extract information from the SRA metadata files
Language:Python37 3 25

linsalrob's Repositories

linsalrob/ComputationalGenomicsManual
Robs manual for the computational genomics and bioinformatics class.
Language:HTML230 11 161
linsalrob/fastq-pair
Match up paired end fastq files quickly and efficiently.
Language:C144 5 2232
linsalrob/PhiSpy
Prediction of prophages from bacterial genomes
Language:Jupyter Notebook73 10 5521
linsalrob/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
Language:Jupyter Notebook39 9 116
linsalrob/sphae
Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!
Language:Python28 5 139
linsalrob/genbank_to
Convert genbank files to a swath of other formats
Language:Python14 4 31
linsalrob/PhageProteomicTree
The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
Language:Perl4 3 0
linsalrob/atavide_lite
A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings maybe specific for our compute resources
Language:Python3 2 11
linsalrob/repeatfinder
fast code for searching for direct and indirect repeats in DNA sequences.
Language:Python3 1 0
linsalrob/alphafold
Open source code for AlphaFold.
Language:Python2 2 0
linsalrob/atavide
Atavistic processing of metagenomics data.
Language:Python2 4 72
linsalrob/genetic_codes
Python code for translating sequences using different NCBI translation tables and genetic codes.
Language:C2 2 0
linsalrob/get_orfs
C code to translate a DNA sequence using different translation tables. Designed to be fast and lightweight, with few dependencies (only zlib and pthreads)
Language:C2 2 0
linsalrob/SUPER-FOCUS
A tool for agile functional analysis of shotgun metagenomic data
Language:Python2 3 0
linsalrob/acacia-stream
testing some streaming using minimap and acacia and something
Language:Python1 2 0
linsalrob/pawsey
Code for running lots of different things on pawsey. This is a bit of a generic bucket and some of the code will be duplicated elsewhere in different projects
Language:Python1 2 0
linsalrob/PhiSigns
PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples
Language:Perl1 4 01
linsalrob/reneo
🦠🧬 Unraveling Viral Genomes from Metagenomes
Language:Python1 0 0
linsalrob/bangers
Convert protein sequences to DNA sequences to make them compatible with mash
Language:C3 0
linsalrob/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell1 0
linsalrob/CF_Data_Analysis
CF Data Analysis
Language:Jupyter Notebook
linsalrob/CompareReferences
Compare References from Google Scholar and ORCID
Language:Python4 0
linsalrob/FOCUS
A model to identify organisms present in metagenomes in seconds
Language:Python3 02
linsalrob/hecatomb
hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
Language:Python1 0
linsalrob/hecatomb-documentation
Documentation for Hecatomb (https://github.com/shandley/hecatomb)
0 0
linsalrob/Koverage
Quickly get coverage statistics given reads and an assembly
Language:Python0 0
linsalrob/PawseySummer2024
Code and ideas for the Pawsey summer internship 2024, designing CNNs for segmented viruses
Language:Jupyter Notebook2 0
linsalrob/phables
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
Language:Python0 0
linsalrob/Phynteny
Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny
Language:PureBasic0 0
linsalrob/prodigal-gv
A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes
Language:C1 0