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orca

:whale: Genomics Research Container Architecture

pass

Proteome Assembler with Short peptide Sequence

pavfinder

:mag: Post Assembly Variants Finder

pavfinder_transcriptome

peekseq

De novo protein-coding potential calculator using a k-mer approach

physlr

:chains: Construct a Physical Map from Linked Reads

picea-engelmannii-plastid

🌲 Annotate the plastid genome of Engelmann spruce (Picea engelmannii)

picea-glauca-plastid

:evergreen_tree: Annotate the plastid genome of white spruce (Picea glauca)

pori

Platform for Oncogenomic Reporting and Interpretation (PORI)

pori_cbioportal

cBioportal adaptor for creating PORI reports in IPR

pori_graphkb_api

REST API for the GraphKB project

pori_graphkb_client

Front-end web client for the GraphKB project

pori_graphkb_loader

The Loaders for GraphKB. Imports content from external sources via the GraphKB REST API

pori_graphkb_parser

A package for parsing and recreating HGVS-like variant notation used in GraphKB

pori_graphkb_python

Python adapter package for querying the GraphKB API

pori_graphkb_schema

Shared package between the API and GUI for GraphKB which holds the schema definitions and schema-related functions

pori_ipr_api

Integrated Pipeline Reports (IPR) API, the reporting API as part of the PORI platform

pori_ipr_client

Integrated Pipeline Reports (IPR) client. The web interface for the reporting application as part of PORI

pori_ipr_python

Python adapter for generating reports uploaded to IPR using the PORI platform

probegenerator

Determine the nucleotide sequences of mutations

pyvcf

A Variant Call Format reader for Python.

qupath-annotation-exchange

An extension for QuPath for importing JSON annotations made in a GSC internal application

rails

🚝RAILS and 👞🔨Cobbler: Assembly Improvement by Long Sequence Scaffolding/Gap-filling

rampage

rAMPage: Rapid AMP Annotation and Gene Estimation

rna-bloom

:hibiscus: reference-free transcriptome assembly for short and long reads

rna-scoop

:shipit: interactive visualization of single-cell transcriptomes

rnabloom2_manuscript

rnaseq_utils

utility scripts for RNA-seq data

rsempipeline

A pipeline for running rsem analysis on thousands of samples

rsemreport

A Django site for reporting the progress of rsempipeline analysis