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    61 repositories

    • CFEIntact

      Public
      A bioinformatics tool for detecting defects in HIV-1 proviral sequences.
      pythonbioinformaticspipeline
      pythonbioinformaticspipelinegenomicsgeneticsgeneshivgenotypevirologyprovirus
      Python
      •
      MIT License
      •4•2•8•5•Updated Apr 21, 2026Apr 21, 2026

    • miseqinteropreader

      Public
      Parser for Illumina MiSeq InterOp binary files
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • sds-viewer

      Public
      Public record of BC CfE Safety Data Sheets (SDS)
      Python
      •0•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • MiCall

      Public
      Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C
      pythonbioinformaticsresistance
      pythonbioinformaticsresistancefastqgenotype
      Python
      •
      GNU Affero General Public License v3.0
      •11•19•115•2•Updated Apr 17, 2026Apr 17, 2026

    • aligntools

      Public
      A Python library for manipulation of CIGAR, MSA, and other alignment formats.
      Python
      •
      GNU Affero General Public License v3.0
      •0•11•1•0•Updated Apr 14, 2026Apr 14, 2026

    • proviral

      Public
      Python
      •
      MIT License
      •2•0•3•1•Updated Apr 9, 2026Apr 9, 2026

    • make_tree

      Public
      Simple script for drawing phylogenetic trees
      Python
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Mar 24, 2026Mar 24, 2026

    • gotoh

      Public
      Simple sequence aligner with high-level language bindings.
      Ruby
      •0•0•0•1•Updated Mar 20, 2026Mar 20, 2026

    • hla_algorithm

      Public
      Reimplementation of a bblab ruby script in python.
      Python
      •0•0•3•0•Updated Mar 19, 2026Mar 19, 2026

    • multicsv

      Public
      A Python library for handling multi-CSV format.
      Python
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Feb 19, 2026Feb 19, 2026

    • bblab-server

      Public
      Useful tools for HIV research from the Brockman and Brumme Lab at SFU
      Python
      •1•0•4•1•Updated Feb 10, 2026Feb 10, 2026

    • pyvdrm

      Public
      Tools for interpreting viral drug resistance mutations
      Python
      •
      GNU Affero General Public License v3.0
      •1•3•0•0•Updated Jan 29, 2026Jan 29, 2026

    • hivstats

      Public
      Various stats about HIV genome, for use in CFEIntact
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jan 23, 2026Jan 23, 2026

    • codeclub1

      Public
      Repository for CFE's first code club session
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jan 19, 2026Jan 19, 2026

    • MiSeqQCReport

      Public
      Quality control report for the MiSeq.
      Perl
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•10•0•Updated Mar 25, 2025Mar 25, 2025

    • react-ferry

      Public
      Tools for integrating a React frontend with a JSON-based REST API
      TypeScript
      •
      MIT License
      •0•0•0•1•Updated Sep 12, 2024Sep 12, 2024

    • cfe-lab.github.io

      Public
      at the BC Centre for Excellence in HIV/AIDS
      1•0•0•0•Updated Jul 24, 2024Jul 24, 2024

    • Kive

      Public
      Archival and automation of bioinformatic pipelines and data
      pythonversion-controlbioinformatics-pipeline
      pythonversion-controlbioinformatics-pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•8•85•19•Updated Jul 23, 2024Jul 23, 2024

    • HIVIntact

      Public archive
      A proviral intactness pipeline.
      Python
      •3•0•0•0•Updated Mar 14, 2024Mar 14, 2024

    • accsense-scrape

      Public
      Download alarm history from temperature sensors
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 14, 2024Feb 14, 2024

    • genetracks

      Public
      Generate track diagrams for genomic alignments
      Python
      •
      MIT License
      •1•0•0•0•Updated Jul 20, 2023Jul 20, 2023

    • tcr-dist

      Public
      Software tools for the analysis of epitope-specific T cell receptor (TCR) repertoires (scroll down for the README)
      Python
      •
      MIT License
      •36•0•0•0•Updated Feb 14, 2023Feb 14, 2023

    • phylodating

      Public
      Python
      •2•1•2•2•Updated Dec 1, 2022Dec 1, 2022

    • qvalue

      Public archive
      p-value to q-value converter for positive false discovery rate (Storey, 2003)
      Python
      •0•0•0•0•Updated Apr 26, 2022Apr 26, 2022

    • text-to-columns

      Public archive
      Split a string of text into columns of its characters
      SCSS
      •0•0•1•0•Updated Apr 26, 2022Apr 26, 2022

    • guava-layout

      Public archive
      HTML
      •0•0•0•0•Updated Apr 26, 2022Apr 26, 2022

    • sequencing-layout

      Public archive
      JavaScript
      •0•0•0•0•Updated Apr 26, 2022Apr 26, 2022

    • quality-check

      Public archive
      Detects find any problems in unaligned nucleotide sequences.
      Python
      •0•0•1•0•Updated Apr 26, 2022Apr 26, 2022

    • unique-sequence

      Public archive
      Identifies unique and identical DNA and amino acid sequences.
      Python
      •0•0•1•0•Updated Apr 26, 2022Apr 26, 2022

    • variable-function

      Public archive
      Performs a statistical test (Mann-Whitney U) on a given set of data.
      SCSS
      •0•0•0•0•Updated Apr 26, 2022Apr 26, 2022
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