All

53 repositories

genomics-workspace
Public
Django website project for common sequence search tools.
django bioinformatics genomics
django bioinformatics genomics django-application blast sequence-alignment ncbi-blast hmmer genomics-visualization clustal
JavaScript
•
Other
•5•17•25•63•Updated Apr 9, 2026Apr 9, 2026
NAL_RNA_seq_annotation_pipeline
Public
Python
•
Other
•4•5•17•2•Updated Feb 24, 2026Feb 24, 2026
GFF3toolkit
Public
Python programs for processing GFF3 files
bioinformatics gff3 gff
bioinformatics gff3 gff gff3-format
Python
•
Other
•27•104•18•1•Updated Dec 15, 2025Dec 15, 2025
i5k-tripal-cypress
Public
JavaScript
•0•0•0•0•Updated Dec 10, 2025Dec 10, 2025
Miniprot_protein_to_genome_alignment
Public
A workflow that aligns protein sequences to a genome (with splice-aware alignment) and generates JBrowse tracks.
Common Workflow Language
•0•0•1•0•Updated Sep 16, 2025Sep 16, 2025
Organism_Onboarding
Public
A workflow to make organism onboarding pipeline easy to handle as an I/O pipeline
pipeline cwl
pipeline cwl
Common Workflow Language
•1•4•5•5•Updated Sep 10, 2025Sep 10, 2025
tripal_eutils
Public
ncbi loader via the eutils interface
ncbi tripal tripal3
ncbi tripal tripal3 tripal3-compatible eutils ncbi-assembly ncbi-biosamples hacktoberfest2022
PHP
•
GNU General Public License v3.0
•3•4•23•2•Updated Mar 15, 2025Mar 15, 2025
ColorByType
Public
A JBrowse plugin to color the features according the feature type
JavaScript
•
Other
•1•2•2•0•Updated Oct 1, 2024Oct 1, 2024
t3_species_glossary
Public
Creates a view to display a glossary of all Tripal 3 organism
PHP
•0•1•1•0•Updated Aug 13, 2024Aug 13, 2024
SRAtoVCF
Public
A pipeline for converting short-read DNA data from SRA into VCF files
Common Workflow Language
•0•0•4•0•Updated Sep 7, 2023Sep 7, 2023
jbrowse-plugin-linkout
Public
TypeScript
•
Apache License 2.0
•0•4•0•0•Updated Aug 29, 2023Aug 29, 2023
Apollo
Public
Customized version of Apollo, which is a genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plu…
Groovy
•
Other
•87•1•0•1•Updated Jun 1, 2023Jun 1, 2023
tripal_elasticsearch
Public
PHP
•
GNU General Public License v3.0
•8•0•0•0•Updated Feb 27, 2023Feb 27, 2023
bam_to_bigwig
Public
Convert your alignment files in BAM format into coverage files in bigWig format
Python
•
Other
•3•0•0•0•Updated Jan 17, 2023Jan 17, 2023
remap-gff3
Public
update gff3 coordinates to new assembly versions
Python
•
Other
•3•8•3•0•Updated Jan 6, 2023Jan 6, 2023
jbrowse
Public
Customized version of jbrowse used for NAL-i5k
JavaScript
•
Other
•0•0•0•34•Updated Dec 10, 2022Dec 10, 2022
jbrowse_track_configs
Public
This is a repository to collect our JBrowse and Apollo track configuration files.
hacktoberfest hacktoberfest2020
hacktoberfest hacktoberfest2020
Shell
•1•0•2•0•Updated Aug 4, 2022Aug 4, 2022
i5k_custom_fields
Public
Provides custom fields for i5k Tripal sites.
PHP
•0•0•0•0•Updated Feb 9, 2022Feb 9, 2022
AgBioData_GFF3_recommendation
Public
The AgBioData GFF3 working group has developed recommendations to solve common problems in the GFF3 format. We suggest improvements for each of the GFF3 fields,…
bioinformatics genomics gff3
bioinformatics genomics gff3 gff
Creative Commons Zero v1.0 Universal
•4•6•3•1•Updated Jan 3, 2022Jan 3, 2022
image_permission_form
Public
This is the blank image permission form needed when submitting projects to the i5k Workspace@NAL.
0•0•0•0•Updated Oct 19, 2021Oct 19, 2021
NAL_CSS
Public
Custom css for the i5k workspace track styles.
CSS
•
Other
•1•0•0•1•Updated Sep 9, 2021Sep 9, 2021
content_onboarding_scripts
Public
Ancillary scripts for onboarding content at the i5k Workspace.
Python
•
Other
•0•0•1•0•Updated Aug 10, 2021Aug 10, 2021
T2-to-T3-Upgrade-Guide
Public
PHP
•1•0•2•0•Updated Jul 16, 2021Jul 16, 2021
gene_jbrowse_field
Public
Create JBrowse field on Tripal 3 Gene Pages
PHP
•
Other
•0•0•4•0•Updated Jun 14, 2021Jun 14, 2021
wiggle-tools
Public
Python
•
Other
•1•0•0•0•Updated Jan 7, 2021Jan 7, 2021
tripal_tests
Public
selenium robot-framework robotframework
selenium robot-framework robotframework selenium-python
Python
•0•0•1•1•Updated Aug 6, 2020Aug 6, 2020
coordinates_conversion
Public
Conversion programs that use the output from fasta_diff.py to convert coordinates and IDs in different format files.
Python
•
Other
•2•1•0•0•Updated Jun 17, 2020Jun 17, 2020
genomics-VM
Public
Setup your development environment for genomics applications easily by setting up a Virtualbox VM through Vagrant.
vagrant virtualbox genomics
vagrant virtualbox genomics virtual-machine
Other
•1•1•11•1•Updated Oct 28, 2019Oct 28, 2019
genomics-workspace_docker
Public
0•0•0•0•Updated Jul 23, 2019Jul 23, 2019
tripal3_organism_layout
Public
a drupal fields module for organism display for i5k
PHP
•0•0•2•0•Updated Apr 9, 2019Apr 9, 2019

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NAL-i5K

All

All

53 repositories

genomics-workspace

NAL_RNA_seq_annotation_pipeline

GFF3toolkit

i5k-tripal-cypress

Miniprot_protein_to_genome_alignment

Organism_Onboarding

tripal_eutils

ColorByType

t3_species_glossary

SRAtoVCF

jbrowse-plugin-linkout

Apollo

tripal_elasticsearch

bam_to_bigwig

remap-gff3

jbrowse

jbrowse_track_configs

i5k_custom_fields

AgBioData_GFF3_recommendation

image_permission_form

NAL_CSS

content_onboarding_scripts

T2-to-T3-Upgrade-Guide

gene_jbrowse_field

wiggle-tools

tripal_tests

coordinates_conversion

genomics-VM

genomics-workspace_docker

tripal3_organism_layout

All

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Repositories list

53 repositories