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    20 repositories

    • bergmanlab.github.io

      Public
      JavaScript
      •1•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • STELR

      Public
      STELR is Snakemake-enabled bioinformatics system for detecting transposable elements in long read sequencing data.
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated May 24, 2024May 24, 2024

    • mcclintock

      Public
      Meta-pipeline to identify transposable element insertions using next generation sequencing data
      Python
      •30•96•8•0•Updated Jan 16, 2024Jan 16, 2024

    • TELR

      Public
      TELR is a fast non-reference transposable element detector from long read sequencing data.
      Python
      •
      BSD 2-Clause "Simplified" License
      •11•33•7•0•Updated Jul 27, 2023Jul 27, 2023

    • ngs_te_mapper2

      Public
      Software for detecting transposable element insertions from next-generation sequencing data
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•9•2•0•Updated Feb 24, 2023Feb 24, 2023

    • enrichmenTE

      Public
      Software for the analysis of LTR retrotransposon insertions in PCR-enriched NGS samples
      Python
      •0•1•0•0•Updated Feb 15, 2023Feb 15, 2023

    • yeast-transposons

      Public
      Saccharomyces transposable element canonical sequences
      Shell
      •
      Creative Commons Zero v1.0 Universal
      •0•4•0•0•Updated Jan 17, 2023Jan 17, 2023

    • drosophila-transposons

      Public
      Drosophila transposable element canonical sequences
      Rich Text Format
      •
      Creative Commons Zero v1.0 Universal
      •11•28•15•0•Updated Jul 11, 2022Jul 11, 2022

    • TIDAL

      Public
      Perl
      •
      MIT License
      •2•0•0•0•Updated Jun 11, 2021Jun 11, 2021

    • ngs_te_mapper

      Public
      Software for detecting transposable element insertions from next-generation sequencing data
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •6•14•0•0•Updated Mar 12, 2021Mar 12, 2021

    • samplot

      Public
      Plot structural variant signals from many BAMs and CRAMs
      Python
      •69•1•0•0•Updated Jan 31, 2019Jan 31, 2019

    • biocontext

      Public
      BioContext is a text mining system for extracting information about molecular processes in biomedical articles.
      Java
      •1•0•0•0•Updated Oct 13, 2015Oct 13, 2015

    • getm

      Public
      GETM is a tool which is capable of extracting information about the expression of genes from biomedical literature
      Java
      •2•1•0•0•Updated Oct 13, 2015Oct 13, 2015

    • linnaeus

      Public
      Species name recognition and normalization software.
      Java
      •
      Other
      •1•3•0•0•Updated Oct 13, 2015Oct 13, 2015

    • blogscripts

      Public
      Scripts used in Bergman Lab blog posts
      Shell
      •0•0•1•0•Updated Apr 18, 2015Apr 18, 2015

    • contemplate

      Public
      Python
      •0•1•0•0•Updated Feb 25, 2015Feb 25, 2015

    • flyfig

      Public
      A utility to plot numerical data on a Dipteran body plan
      R
      •1•3•0•0•Updated Jan 20, 2015Jan 20, 2015

    • ecologIE

      Public
      Tools for information extraction from the ecological literature
      Shell
      •1•6•1•0•Updated Sep 3, 2014Sep 3, 2014

    • MartScript

      Public
      A scripting language for automatically creating BioMarts.
      Java
      •
      GNU Lesser General Public License v2.1
      •2•1•0•0•Updated May 19, 2011May 19, 2011

    • biomart-plus-extras

      Public
      An extended version of BioMart 0.7 (www.biomart.org).
      Perl
      •
      GNU Lesser General Public License v2.1
      •3•1•0•0•Updated May 14, 2011May 14, 2011