jhuanglab / bioinstaller Goto Github PK
View Code? Open in Web Editor NEWA comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform
License: Other
A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform
License: Other
Configuration file: github.toml
Description: VariantTools, software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis.
[varianttools]
github_url = "https://github.com/vatlab/VariantTools"
install = "pip install ."
Configuration file: github.toml
Description: "This Snakemake pipeline implements the GATK best-practices workflow"
[snakemake_dna_gatk_flow]
github_url = "https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling"
Configuration file: nongithub.toml
Description: effusion, A method for predicting protein function, Effusion, that uses a sequence similarity network to add context for homology transfer, a probabilistic model to account for the uncertainty in labels and function propagation, and the structure of the Gene Ontology (GO) to best utilize sparse input labels and make consistent output predictions. Effusion's model makes it practical to integrate rare experimental data and abundant primary sequence and sequence similarity.
Homepage: http://www.babbittlab.ucsf.edu/effusion/
Publication: Effusion: Prediction of Protein Function from Sequence Similarity Networks. Bioinformatics. 2018 Aug 01, PMID: 30084920 DOI: 10.1093/bioinformatics/bty672
[effusion]
source_url = "http://www.babbittlab.ucsf.edu/effusion/effusion_{{version}}.tar.gz"
version_available = ["1.0.0"]
Hello,
We were trying to load the app in the web server after the installation of shiny and BioInstaller. We are getting the URL path for loading the page on web server, but it is not getting loaded. Please find the attachment of the error we are facing.
Any help regarding this is appreciated.
Thank you!
Dear All,
How can we build pipeline using BioInstaller after the installation of tools/software?
Using the tools mentioned below
I am trying to build a transcriptome pipeline using BioInstaller. There are no manual/ procedure for building pipeline.
Any help regarding this would be appreciated!
Thanks & Regards
Anoopa
I guess it is better to discuss all off-topic theme in this post.
The main aim of this forum is to provide a fully free place sharing the bioinformatics tools/scripts and databases. The resources recorded in the posts will be integrated into the BioInstaller configuration files. Please read this post when you want to submit a new post in this forum.
Required fields: author name., title. journal, year, project URL, tags
There is three part required for uploading a new BioInstaller item:
Demo 1:
Configuration file: github.toml
description: GATK variant calling workflow based on [snakemake] (https://snakemake.readthedocs.io/en/stable/)
publication: Not yet
[snakemake_dna_gatk_flow]
github_url = "https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling"
Demo 2:
Configuration file: nongithub.toml
description: Mirror URL of GATK4
[gatk4_jhuang_mirror]
source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/gatk/gatk-{{version}}.zip"
version_available = ["4.0.6.0", "4.0.0.0"]
I will integrate the items written in this post to my Bioinformatics-Resources project.
Configuration file: nongithub.toml
Description: HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data
[hgtid]
source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/hgtid/{{version}}"
version_available = ["HGT-ID_v1.0.tar.gz", "sampleResults.zip"]
Configuration file: db_main.toml
Description: miRDB is an online database for miRNA target prediction and functional annotations.
[db_mirdb]
source_url = "http://mirdb.org/download/miRDB_v{{version}}_prediction_result.txt.gz"
version_avaliable = ["5.0", "4.0", "3.0", "2.0", "1.0"]
Configuration file: github.toml
Description: "mRNN is an implementation of a Gated Recurrent Unit (GRU) network for classification of transcripts as either coding or noncoding."
[mrnn]
github_url = "https://github.com/hendrixlab/mRNN"
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