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    29 repositories

    • iprgc_trap_analyses

      Public
      TeX
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • macrophage_response_lpanamensis

      Public
      singularity container comprising analyses of macrophages infected with Leishmania panamensis.
      TeX
      •1•0•0•0•Updated Sep 8, 2025Sep 8, 2025

    • cure_fail_host_analyses

      Public
      Container recipe for repeating the L.panamensis cure/fail analyses in the host.
      TeX
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 10, 2025Mar 10, 2025

    • dantools

      Public
      Utilities to compare disparate genomes
      Perl
      •
      Other
      •2•2•0•0•Updated Dec 5, 2024Dec 5, 2024

    • fe_adipocyte_analyses

      Public
      TeX
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 11, 2024Nov 11, 2024

    • clinical_strains_analyses

      Public
      TeX
      •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

    • hpgltools_singularity

      Public
      Emacs Lisp
      •
      GNU General Public License v3.0
      •1•0•0•1•Updated May 14, 2024May 14, 2024

    • hpgltools

      Public
      A collection of R functions to aid in host-pathogen genomic research
      visualizationannotationsbioconductor
      visualizationannotationsbioconductorrna-seq-analysisontology-searchplotting-in-rpathogen-genomics
      R
      •
      Other
      •12•12•0•1•Updated May 8, 2024May 8, 2024

    • clinical_strains_lpanamensis

      Public
      singularity container comprising the comparison of some clinical strains
      Shell
      •1•0•0•0•Updated Apr 24, 2024Apr 24, 2024

    • CL_biopsies_Colombia

      Public
      container recipe to perform analyses examining cutaneous leishmania biopsies with CIDEIM published approximately 202310
      Emacs Lisp
      •
      GNU General Public License v2.0
      •2•0•0•0•Updated Apr 24, 2024Apr 24, 2024

    • CYOA

      Public
      Perl
      •
      Other
      •2•1•0•0•Updated Dec 11, 2023Dec 11, 2023

    • tmrc_metabolome

      Public
      Some shared information from the TMRC metabolomics experiment
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 19, 2022Jan 19, 2022

    • rnaseq_kajal_2020

      Public
      HTML
      •2•0•0•0•Updated Sep 2, 2020Sep 2, 2020

    • coex-network-optimization-construction

      Public
      Code for submitting co-expression network construction jobs to a cluster and summarizing the results
      Shell
      •0•0•0•0•Updated Jun 5, 2019Jun 5, 2019

    • manuscript-shared-rnaseq

      Public
      R and Rmarkdown code used across multiple RNA-Seq projects.
      R
      •6•2•0•0•Updated Jun 4, 2019Jun 4, 2019

    • tryp-reg-predict

      Public
      Trypanosomatid Regulatory Element Prediction Pipeline
      Python
      •0•0•0•0•Updated Apr 21, 2019Apr 21, 2019

    • manuscript-coex-networks

      Public
      Functional enrichment analysis of individual and ensemble co-expression networks
      Makefile
      •0•0•0•0•Updated Mar 25, 2019Mar 25, 2019

    • tnseq_spyogenes_2017

      Public
      TNSeq analyses on Streptococcus pyogenes strain 5448 performed in 2017.
      HTML
      •1•0•0•0•Updated Jan 18, 2019Jan 18, 2019

    • utr_analysis

      Public
      Pipeline for determining the 5'UTR spliced leader and 3'UTR poly-A acceptor sites in a collection of RNA-Seq reads
      Python
      •4•8•2•0•Updated Nov 15, 2017Nov 15, 2017

    • spirogyra_assembly

      Public
      A relatively minimal de-novo algal RNA assembly.
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 10, 2017Nov 10, 2017

    • TxDb.TcruziCLBrenerEsmer.tritryp32.genes

      Public
      Transcript annotation package for T. cruzi strain CL Brener Esmeraldo-like haplotype
      R
      •0•0•0•0•Updated May 12, 2017May 12, 2017

    • TxDb.LmajorFriedlin.tritryp32.genes

      Public
      Transcript annotation package for Leishmania major strain Friedlin
      R
      •0•0•0•0•Updated May 12, 2017May 12, 2017

    • org.TcCLB.esmer.tritryp.db

      Public
      Genome wide annotations for Trypanosoma cruzi strain Friedlin Esmeraldo-like
      R
      •0•0•0•0•Updated May 12, 2017May 12, 2017

    • gene-structure-analysis

      Public
      Visualization and descriptive statistics of Trypanosome gene structure using RNA-Seq data.
      R
      •0•0•0•0•Updated May 11, 2017May 11, 2017

    • ptu-detection

      Public
      A simple script for detecting polycistronic transcriptional units (PTUs) in Trypanosomatid genomes.
      Python
      •0•0•0•0•Updated Dec 25, 2016Dec 25, 2016

    • gene-structure-determination

      Public
      Gene structure determination and novel ORF detection using RNA-Seq data
      Python
      •0•0•0•0•Updated Nov 28, 2016Nov 28, 2016

    • fetch-eupathdb-resources

      Public
      Shell script to retrieve specific resources (FASTA, GFF, etc.) from TriTrypDB for a given set of species
      Shell
      •0•0•0•0•Updated Sep 9, 2016Sep 9, 2016

    • utr_length_composition_and_site_usage_analysis

      Public
      UTR Length, Composition, and Alternative Trans-splicing / Poly-adenylation Analysis
      R
      •0•0•0•0•Updated Jul 8, 2016Jul 8, 2016

    • lmajor_alternate_acceptor_site_usage

      Public
      Analysis comparing the use of alternative trans-splicing and alternative-polyadenylation sites across developmental stages in Leishmania major
      0•0•0•0•Updated Feb 2, 2015Feb 2, 2015
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