Extension module docs: Added UofS-Pulse-Binfo modules.

docs/extensions/3rdparty.rst

@@ -14,7 +14,7 @@ This module provides a basic interface to allow your users to utilize your serve
 Tripal Galaxy
 -------------
 
-This module is for integration of Tripal and the Galaxy Project. It facillitates the creation of forms on your Tripal site that submit jobs to a galaxy instance.
+This module is for integration of Tripal and the Galaxy Project. It facilitates the creation of forms on your Tripal site that submit jobs to a galaxy instance.
 
 `Documentation <https://github.com/tripal/tripal_galaxy/blob/7.x-1.x/README.md>`__
 `Repository <https://github.com/tripal/tripal_galaxy>`__
@@ -26,3 +26,11 @@ This module provides integration between Tripal sites and pre-existing GMOD JBro
 
 `Documentation <https://github.com/tripal/tripal_jbrowse/blob/7.x-2.1.x/README.md>`__
 `Repository <https://github.com/tripal/tripal_jbrowse>`__
+
+VCF Filter
+-----------
+
+This modules provides a form interface so users can custom filter existing VCF files and export in a variety of formats. The form simply provides an interface to VCFtools and uses the Tripal Download API to provide the filtered file to the user.
+
+`Documentation <https://github.com/UofS-Pulse-Binfo/vcf_filter/blob/master/README.md>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/vcf_filter>`__

docs/extensions/datainput.rst

@@ -3,6 +3,14 @@ Data Loading/Collection
 
 The following modules provide interfaces for collection and/or loading of biological data.
 
+Genotype Loader
+----------------
+
+A Drush-based loader for VCF files that follows the genotype storage rules outline by ND genotypes. It has been optimized to handle very large files and supports customization of ontology terms used.
+
+`Documentation <https://genotypes-loader.readthedocs.io/en/latest/>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/genotypes_loader>`__
+
 Mainlab Chado Loader
 ---------------------
 
@@ -11,6 +19,22 @@ MCL (Mainlab Chado Loader) is a module that enables users to upload their biolog
 `Documentation <https://gitlab.com/mainlabwsu/mcl/blob/master/README.md>`__
 `Repository <https://gitlab.com/mainlabwsu/mcl>`__
 
+Raw Phenotypes
+---------------
+
+This module was designed to aid in collection and further analysis of raw phenotypic data. It supports Excel drag-n-drop uploads with immediate validation and researcher feedback. Additionally, it provides summary charts and download functionality.
+
+`Documentation <https://github.com/UofS-Pulse-Binfo/rawphenotypes/blob/master/README.md>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/rawphenotypes>`__
+
+Tripal BibTeX
+--------------
+
+A BibTEX importer for Tripal Publications. Currently this module only provides a drush function (tripal-import-bibtex-pubs; trpimport-bibtex) for import of BibTEX files.
+
+`Documentation <https://github.com/UofS-Pulse-Binfo/tripal_bibtex/blob/7.x-3.x/README.md>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/tripal_bibtex>`__
+
 Tripal Plant PopGen Submission
 -------------------------------
 

docs/extensions/visualization.rst

@@ -3,6 +3,22 @@ Visualization/Display
 
 The following modules provide specialized displays for Tripal content types.
 
+Analyzed Phenotypes
+--------------------
+
+This module provides support and visualization for partially analyzed data stored in a modified GMOD Chado schema. It is meant to support large scale phenotypic data through backwards compatible improvements to the Chado schema including the addition of a project and stock foreign key to the existing phenotype table, optimized queries and well-choosen indexes.
+
+`Documentation <https://analyzedphenotypes.readthedocs.io/en/latest/index.html>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/analyzedphenotypes>`__
+
+CvitEmbed
+----------
+
+This module integrates `CViTjs <https://github.com/LegumeFederation/cvitjs>`__ with Tripal to provide whole-genome visualizations. It creates one page per plot and makes them accessible via the Drupal Navigation menu.
+
+`Documentation <https://github.com/UofS-Pulse-Binfo/cvitembed/blob/master/README.md>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/cvitembed>`__
+
 Mainlab Tripal Data Display
 ----------------------------
 
@@ -11,6 +27,14 @@ Mainlab Tripal Data Display contains a set of Drupal/PHP templates that organize
 `Documentation <https://gitlab.com/mainlabwsu/mainlab_tripal/blob/master/README.md>`__
 `Repository <https://gitlab.com/mainlabwsu/mainlab_tripal>`__
 
+ND Genotypes
+-------------
+
+This module provides support and visualization of genotypic data stored in a modified GMOD Chado schema. The 3.x branch of this module represents a shift towards support for large scale genotypic datasets through backwards compatible improvements to the Chado schema including a new gathering table for genotypes (genotype_call) modeled after the chado phenotype table, optimized queries and well-choosen indexes.
+
+`Documentation <https://nd-genotypes.readthedocs.io/en/latest/>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/nd_genotypes>`__
+
 Tripal Fancy Fields
 -------------------