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    31 repositories

    • NeuroMabSeq

      Public
      A place to track issues for NeuroMabSeq project
      Jupyter Notebook
      •1•2•5•0•Updated Aug 5, 2024Aug 5, 2024

    • clonalvdjseq

      Public
      HTML
      •0•0•0•0•Updated May 20, 2024May 20, 2024

    • scRNA_shiny

      Public
      scRNA-seq Shiny App
      R
      •
      Apache License 2.0
      •6•13•1•0•Updated May 1, 2023May 1, 2023

    • survey-pie-chart

      Public
      JavaScript
      •0•0•0•0•Updated Jul 26, 2022Jul 26, 2022

    • scRNA-seq

      Public
      0•0•0•0•Updated Jun 26, 2021Jun 26, 2021

    • assemblathon2-analysis

      Public
      collection of scripts and commands used by Ian Korf, Keith Bradnam, and Joe Fass in the analysis of Assemblathon 2 entries (assemblies)
      Perl
      •21•21•2•2•Updated Mar 29, 2021Mar 29, 2021

    • HTStream_reports

      Public
      R reports based on JSON HTStream ouptut
      Apache License 2.0
      •0•1•0•0•Updated May 4, 2020May 4, 2020

    • module_counter

      Public
      Python
      •0•0•0•0•Updated Feb 29, 2020Feb 29, 2020

    • django-ezreg

      Public
      Python
      •3•0•0•0•Updated Jan 22, 2020Jan 22, 2020

    • scRNAseq_Analysis_Workflow

      Public
      multipart analysis workflow in R for scRNAseq
      0•1•0•0•Updated Nov 1, 2019Nov 1, 2019

    • proc10xG

      Public
      processing 10x genomics reads
      Python
      •
      Apache License 2.0
      •12•24•3•0•Updated Oct 27, 2019Oct 27, 2019

    • ucdbioinfo_supernova_pipeline

      Public
      10x genomics supernova pipeline for running on UCD Bioinformatics Core cluster
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 17, 2019Sep 17, 2019

    • split-freebayes

      Public
      scripts to split freebayes run into multiple jobs
      Perl
      •0•0•0•0•Updated Aug 14, 2019Aug 14, 2019

    • bcl2fastq_automation

      Public
      automating bcl2fastq running
      Perl
      •0•0•0•0•Updated Jun 21, 2019Jun 21, 2019

    • proc10xSC

      Public
      Processing 10x Genomics Single Cell data
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Aug 10, 2018Aug 10, 2018

    • OptimA

      Public
      Tool to find optimal assembly using the miniasm long read assembler.
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 12, 2018Jul 12, 2018

    • scythe

      Public
      A 3'-end adapter contaminant trimmer
      C
      •
      MIT License
      •38•11•1•1•Updated Jan 23, 2018Jan 23, 2018

    • RnaVis

      Public
      Shiny application to Visualize RNAseq data
      R
      •
      Apache License 2.0
      •1•2•2•0•Updated Jan 22, 2018Jan 22, 2018

    • taxonomy_conversion

      Public
      scripts to convert qiime taxonomy format to RDP format
      Go
      •1•0•0•0•Updated Dec 29, 2017Dec 29, 2017

    • Report-templates

      Public
      template R markdown files for reporting results
      0•0•0•0•Updated Nov 21, 2017Nov 21, 2017

    • Preprocessing-Pipeline

      Public
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 18, 2017Oct 18, 2017

    • PacBio_GenomeStats

      Public
      Given a set of Pac Bio cells, generate fofn needed for assembly and statistics
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Sep 18, 2017Sep 18, 2017

    • ucd_bcl2fastq2

      Public
      automated handling of bcl2fastq2 in the ucd environment
      Apache License 2.0
      •0•0•0•0•Updated Dec 28, 2016Dec 28, 2016

    • biocore-tools

      Public
      Collection of scripts and tools used within the UC Davis Bioinformatics Core
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Jul 27, 2016Jul 27, 2016

    • workshop-template

      Public
      template for bioinformatics workshop documentation using jekyll + markdown
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Jul 21, 2016Jul 21, 2016

    • sickle

      Public
      Windowed Adaptive Trimming for fastq files using quality
      C
      •
      MIT License
      •95•25•0•0•Updated Feb 25, 2015Feb 25, 2015

    • PBcR-testing

      Public
      framework for testing various strategies related to correction of PacBio reads (via Illumina reads) and subsequent use in assembly
      0•1•0•0•Updated Apr 23, 2013Apr 23, 2013

    • sabre

      Public
      A barcode demultiplexing and trimming tool for FastQ files
      C
      •
      MIT License
      •20•1•0•0•Updated May 30, 2012May 30, 2012

    • qrqc

      Public
      Quick Read Quality Control
      R
      •7•5•0•0•Updated May 30, 2012May 30, 2012

    • alignerviz

      Public
      A simple tool to visualize sequences using Vlachos et al's technique
      Python
      •2•8•0•0•Updated Feb 10, 2011Feb 10, 2011