{"id":18,"date":"2021-04-14T14:01:46","date_gmt":"2021-04-14T14:01:45","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/template\/help-sheets\/"},"modified":"2024-03-01T13:07:35","modified_gmt":"2024-03-01T13:07:35","slug":"help-sheets","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/human-ecosystems-materials\/help-sheets\/","title":{"rendered":"Technical help sheets"},"content":{"rendered":"\n

Technical requirements for data analysis<\/h2>\n\n\n\n

You will require the following tools for executing the practicals in this course:<\/p>\n\n\n\n

Accessing human cohort data at EGA<\/strong><\/p>\n\n\n\n

SAMtools<\/td>https:\/\/www.htslib.org\/<\/a><\/td><\/tr>
BCFTools<\/td>https:\/\/samtools.github.io\/bcftools\/bcftools.html<\/a><\/td><\/tr>
PyEGA3<\/td>https:\/\/github.com\/EGA-archive\/ega-download-client<\/a><\/td><\/tr>
IGV (User interface)<\/td>https:\/\/www.igv.org\/<\/a><\/td><\/tr>
QuickView<\/td>https:\/\/github.com\/EGA-archive\/ega-quickview<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

GWAS catalog<\/strong><\/p>\n\n\n\n

Default command line\/terminal<\/td><\/tr>
Any web browser<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

Polygenic risk scores<\/strong> – Sam Lambert<\/p>\n\n\n\n

Rstudio<\/td>https:\/\/posit.co\/download\/rstudio-desktop\/<\/a><\/td><\/tr>
nextflow<\/td>https:\/\/www.nextflow.io\/<\/a><\/td><\/tr>
pgsc_calc<\/td>https:\/\/pgsc-calc.readthedocs.io\/en\/latest\/<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

Integrated omics, epi-genomics, and biological age<\/strong><\/p>\n\n\n\n

Rstudio<\/td>https:\/\/posit.co\/download\/rstudio-desktop\/<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n","protected":false},"excerpt":{"rendered":"

Technical requirements for data analysis You will require the following tools for executing the practicals in this course: Accessing human cohort data at EGA SAMtools https:\/\/www.htslib.org\/ BCFTools https:\/\/samtools.github.io\/bcftools\/bcftools.html PyEGA3 https:\/\/github.com\/EGA-archive\/ega-download-client IGV (User interface) https:\/\/www.igv.org\/ QuickView https:\/\/github.com\/EGA-archive\/ega-quickview GWAS catalog Default command line\/terminal Any web browser Polygenic risk scores – Sam Lambert Rstudio https:\/\/posit.co\/download\/rstudio-desktop\/ nextflow https:\/\/www.nextflow.io\/ pgsc_calc…<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":5,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-18","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/human-ecosystems-materials\/wp-json\/wp\/v2\/pages\/18","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/human-ecosystems-materials\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/human-ecosystems-materials\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/human-ecosystems-materials\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/human-ecosystems-materials\/wp-json\/wp\/v2\/comments?post=18"}],"version-history":[{"count":7,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/human-ecosystems-materials\/wp-json\/wp\/v2\/pages\/18\/revisions"}],"predecessor-version":[{"id":1391,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/human-ecosystems-materials\/wp-json\/wp\/v2\/pages\/18\/revisions\/1391"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/human-ecosystems-materials\/wp-json\/wp\/v2\/media?parent=18"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}