» tallphil - Bioinformatics
I've written a handful of bioinformatics tools which are free to use on this site. They are:
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Labrador
- Labrador is a web based tool to manage projects and automate the processing of publicly available datasets.
Researchers can use it to search through previously processed data, find how it was analysed, read processing reports and download the relevant files to their computers. If a required dataset isn't yet available, they can Create a New Project - this information about the required data sets is then passed on to your resident bioinformaticians, who can process it for you. The status of projects is tracked, and everything is kept together in a logical place.
Administrators (bioinformaticians) can delegate the process of choosing required data to researchers. Labrador automatically retrieves public data accession numbers and can write bash scripts to download and process data. This helps to standardise in-house processing and streamline pipelines.
- Labrador is a web based tool to manage projects and automate the processing of publicly available datasets.
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Cluster Flow
- Cluster Flow is a package written to run bioinformatics processing pipelines in a cluster environment.
Modules can be written in any language and pipelines are defined in simple configuration files. Cluster Flow is called from the command line. Cluster Flow will set off multiple queued jobs on the cluster with queue dependencies as defined in the pipeline.
- Cluster Flow is a package written to run bioinformatics processing pipelines in a cluster environment.
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Sequences
- Fast and simple sequence manipulation tool - see the corresponding dsDNA, reverse compliment, compliment or reverse sequences for any DNA or RNA sequence.
- Further information here: tallphil.co.uk/sequences, github repository here
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Cytobands - retired
- A tool to convert cytogenetic bands to genomic co-ordinates, and vice versa
- Further information here: tallphil.co.uk/cytoband/
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Space Saver
- A short perl script to locate large uncompressed text files
- Further information here: tallphil.co.uk/finding-big-text-files/
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Genome RE Sites - retired
- Apologies, this tool will no longer work (removed due to server space constraints)
- Download the cut site co-ordinates of any restriction enzyme (or indeed, the occurrence of any sequence in the genome)
- Further information and perl script for offline use here: tallphil.co.uk/genome-re-sites/