From cc5c0538cacffd8dc1e7fb510d701fcfae8215f9 Mon Sep 17 00:00:00 2001 From: pnrobinson Date: Sat, 30 Sep 2023 16:57:09 -0400 Subject: [PATCH] badges --- .github/workflows/mkdocs.yml | 1 + docs/assets/stylesheets/custom.css | 7 +++++ docs/software.md | 47 ++++++++++++++++++------------ mkdocs.yml | 2 ++ 4 files changed, 38 insertions(+), 19 deletions(-) create mode 100644 docs/assets/stylesheets/custom.css diff --git a/.github/workflows/mkdocs.yml b/.github/workflows/mkdocs.yml index 523a54f..a8d8f48 100644 --- a/.github/workflows/mkdocs.yml +++ b/.github/workflows/mkdocs.yml @@ -20,4 +20,5 @@ jobs: path: .cache - run: pip install mkdocs-material - run: pip install pillow cairosvg + - run: pip install mkdocs-badges - run: mkdocs gh-deploy --force \ No newline at end of file diff --git a/docs/assets/stylesheets/custom.css b/docs/assets/stylesheets/custom.css new file mode 100644 index 0000000..6343aed --- /dev/null +++ b/docs/assets/stylesheets/custom.css @@ -0,0 +1,7 @@ +.badge.software .title { + background-color: black; +} + +.badge.software .value { + background-color: green; +} diff --git a/docs/software.md b/docs/software.md index 4adbc1a..2f0f546 100644 --- a/docs/software.md +++ b/docs/software.md @@ -11,6 +11,8 @@ Terms in the HPO describe individual phenotypic abnormalities such as atrial sep For further details and information please refer to the [Human Phenotype Ontology Homepage](http://www.human-phenotype-ontology.org). The HPO is developed as a part of the [Monarch Initiative](http://monarchinitiative.org). +S|HPO - GitHub||link:https://github.com/obophenotype/human-phenotype-ontology| + ## The Global Alliance for Health (GA4GH) Phenopacket Schema @@ -23,41 +25,43 @@ The Phenopacket Schema represents an open standard for sharing disease and pheno * [Jacobsen JOB, et al. (2022) The GA4GH Phenopacket schema defines a computable representation of clinical data. Nat Biotechnol. 40:817-820](https://pubmed.ncbi.nlm.nih.gov/35705716/) -* [Danis D,et al. (2023) Phenopacket-tools: Building and validating GA4GH Phenopackets. PLoS One. 18:e0285433](https://pubmed.ncbi.nlm.nih.gov/37196000/); [GitHub repository](https://github.com/phenopackets/phenopacket-tools) - +S|phenopacket-schema - GitHub||link:https://github.com/phenopackets/phenopacket-schema| +* [Danis D,et al. (2023) Phenopacket-tools: Building and validating GA4GH Phenopackets. PLoS One. 18:e0285433](https://pubmed.ncbi.nlm.nih.gov/37196000/); +S|phenopacket-tools - GitHub||link:https://github.com/phenopackets/phenopacket-tools| ## Exomiser The Exomiser is a Java program that functionally annotates and prioritises variants from whole-exome sequencing data starting from a VCF file. The Exomiser was developed by our group, Damian Smedley and Jules Jacobsen of the Mouse Informatics Group at the Sanger Institute (now at the 100,000 Genomes Project and Quenn Mary's University in London), and other members of the [Monarch Initiative](http://monarchinitiative.org). +- [Robinson et al., 2014, Genome Research](https://pubmed.ncbi.nlm.nih.gov/24162188/){:target="_blank"} and [Smedley et al. (2015)](http://www.ncbi.nlm.nih.gov/pubmed/26562621){:target="_blank"} +S|Exomiser - GitHub||link:https://github.com/exomiser/Exomiser| + +- An [online demo version](https://exomiser.monarchinitiative.org/exomiser/) is available -The Exomiser is available for download, and an online demo version is available here. -

Smedley D, Jacobsen JO, Jäger M, Köhler S, Holtgrewe M, Schubach M, Siragusa E, Zemojtel T, Buske OJ, Washington NL, Bone WP, Haendel MA, Robinson PN. (2015). Next-generation diagnostics and disease-gene discovery with the Exomiser. Nature Protocols 10:2004-15.
- PubMed

## Phenomizer -The Phenomizer aims to help clinicians to identify the correct differential diagnosis in the field of human genetics. -The user enters the signs/symptoms of the patient encoded as terms from the Human Phenotype Ontology Homepage. -The software then ranks all diseases from OMIM, Orphanet, and DECIPHER by a score that reflects how well the phenotypic profiles of the patient - and the disease match to each other.

+The [Phenomizer](http://compbio.charite.de/phenomizer) aims to help clinicians to identify the correct differential diagnosis +in the field of human genetics. +The user enters the signs/symptoms of the patient encoded as terms from the +[HPO](http://www.human-phenotype-ontology.org). +The software then ranks all diseases from OMIM, Orphanet, and DECIPHER by a score that reflects how well the phenotypic profiles of the patient and the disease match to each other. -

Kohler, S., Schulz, M. H., Krawitz, P., Bauer, S., Dolken, S., Ott, C. E., Mundlos, C., Horn, D., Mundlos, S., and Robinson, P. N. (2009). Clinical diagnostics in human genetics with semantic similarity searches in ontologies. Am. J. Hum. Genet. 85, 457–464.
PubMed -

+- See also [Kohler, S. et al., 2009](http://www.ncbi.nlm.nih.gov/pubmed/19800049) - ## ChIP-seq software Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) is a powerful technology to identify the genome-wide locations of transcription factors and other DNA binding proteins. Computational ChIP-seq peak calling infers the location of protein-DNA interactions based on various measures of enrichment of sequence reads. Our algorithm, Q, uses an assessment of the quadratic enrichment of reads to center candidate peaks followed by statistical analysis of saturation of candidate peaks by 5' ends of reads. We show that our method not only is substantially faster than several competing methods but also demonstrates statistically significant advantages with respect to reproducibility of results and in its ability to identify peaks with reproducible binding site motifs. -* [Hansen P, et al. (2015) Saturation -analysis of ChIP-seq data for reproducible identification of binding peaks. Genome Res 25:1391-400.](http://www.ncbi.nlm.nih.gov/pubmed/26163319); [GitHub repository](https://github.com/charite/Q) +- [Hansen P, et al. (2015) Saturation +analysis of ChIP-seq data for reproducible identification of binding peaks. Genome Res 25:1391-400.](http://www.ncbi.nlm.nih.gov/pubmed/26163319) +S|Q - GitHub||link:https://github.com/charite/Q| * [Hansen P, et al. (2016) Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus. BMC Genomics 17:873](https://pubmed.ncbi.nlm.nih.gov/27814676/) @@ -65,11 +69,16 @@ analysis of ChIP-seq data for reproducible identification of binding peaks. Geno ## IMSEQ--a fast and error aware approach to immunogenetic sequence analysis -

Recombined T- and B-cell receptor repertoires are increasingly being studied using next generation sequencing (NGS) in order to interrogate the repertoire composition as well as changes in the distribution of receptor clones under different physiological and disease states. This type of analysis requires efficient and unambiguous clonotype assignment to a large number of NGS read sequences, including the identification of the incorporated V and J gene segments and the CDR3 sequence. Current tools have deficits with respect to performance, accuracy and documentation of their underlying algorithms and usage.

-

IMSEQ is a method to derive clonotype repertoires from NGS data with sophisticated routines for handling errors stemming from PCR and sequencing artefacts. The application can handle different kinds of input data originating from single- or paired-end sequencing in different configurations and is generic regarding the species and gene of interest.

-

The software can be downloaded from the project homepage.

-

Kuchenbecker, L., Nienen, M., Hecht, J., Neumann, A. U., Babel, N., Reinert, K., and Robinson, P. N. (2015). IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. Bioinformatics, .
PubMed -

+Recombined T- and B-cell receptor repertoires are increasingly being studied using next generation sequencing (NGS) in order to interrogate the repertoire composition as well as changes in the distribution of receptor clones under different physiological and disease states. +This type of analysis requires efficient and unambiguous clonotype assignment to a large number of NGS read sequences, +including the identification of the incorporated V and J gene segments and the CDR3 sequence. +Current tools have deficits with respect to performance, accuracy and documentation of their underlying algorithms and usage. +IMSEQ is a method to derive clonotype repertoires from NGS data with sophisticated routines for handling errors stemming +from PCR and sequencing artefacts. The application can handle different kinds of input data originating from single- or +paired-end sequencing in different configurations and is generic regarding the species and gene of interest. +The software can be downloaded from the [project homepage](https://www.imtools.org). + +- See also [Kuchenbecker, L. et al., 2015](http://www.ncbi.nlm.nih.gov/pubmed/25987567). diff --git a/mkdocs.yml b/mkdocs.yml index 32a4721..06b8f3d 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -29,6 +29,8 @@ theme: plugins: - social + - badges: + extra: social: