sfletc
Bioinformatics Research Fellow at the QAAFI, University of Queensland, Australia. Specialise in bioinformatics, data science, software development and RNAi.
University of QueenslandUQ, St Lucia, Australia
Pinned Repositories
3d_prints
STL files for 3D printing
bioconda-recipes
Conda recipes for the bioconda channel.
data_tutorials
iPython notebooks for workshops
scram2plot
Python scripts for plotting scram2 alignments
scramAligner
The scramAligner pipeline is designer to align small RNA reads to references sequences with no mis-matches. There is no requirement for reference index building. The pipeline is ideally suited to analysis of siRNAs generated from transgenes or viruses. Scripts for visualising alignments are also provided
scramTrimmer
Small RNA read adaptor trimmer - fast, trims NEXTflex reads in one step, compressed FASTQ input and output
siRNAenricher
Identify genomic regions with siRNA enrichment
sfletc's Repositories
sfletc/3d_prints
STL files for 3D printing
sfletc/bioconda-recipes
Conda recipes for the bioconda channel.
sfletc/data_tutorials
iPython notebooks for workshops
sfletc/scram2plot
Python scripts for plotting scram2 alignments
sfletc/scramAligner
The scramAligner pipeline is designer to align small RNA reads to references sequences with no mis-matches. There is no requirement for reference index building. The pipeline is ideally suited to analysis of siRNAs generated from transgenes or viruses. Scripts for visualising alignments are also provided
sfletc/scramTrimmer
Small RNA read adaptor trimmer - fast, trims NEXTflex reads in one step, compressed FASTQ input and output
sfletc/siRNAenricher
Identify genomic regions with siRNA enrichment
sfletc/bioinformatics_docker_files
Docker files for building bioinformatics working environments
sfletc/functional_siRNA_tutorial
Google collab tutorial for bioinformatics analysis of dsRNA processing and functional siRNAs
sfletc/logomaker
Software for the visualization of sequence-function relationships
sfletc/Micro_Bit_Weather_Bit
Add on weather station module for the micro:bit ecosystem.
sfletc/pi-timelapse
Time-lapse app for Raspberry Pi computers.
sfletc/PyBioUtils
Python bioinformatics utils
sfletc/pycopy-lib
Standard library of the Pycopy project, minimalist and light-weight Python language implementation
sfletc/scram
Fast and simple small RNA read alignment and visualisation
sfletc/scram2
Updated and integrated small RNA exact match aligner and visualisation pipeline
sfletc/scram2Wig
Convert scram2Aligner output CSV files to WIG files showing mean coverage at each position. These can be loaded into GBROWSE sessions.
sfletc/scram_docker
The scram aligner, scram_plot plotting package & Jupyter Notebook on the minimal Miniconda base
sfletc/scram_plot
scram2_plot: generate profiles and interactive scatter plots from scram2 alignments
sfletc/scram_worked_example
scram_worked_example
sfletc/scramEnricher
Identify regions of enriched siRNAs or miRNAs
sfletc/scramPkg
sfletc/thingsboard.github.io
Documentation repository