{"id":18,"date":"2021-04-14T14:01:45","date_gmt":"2021-04-14T14:01:45","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/template\/help-sheets\/"},"modified":"2023-06-22T10:11:40","modified_gmt":"2023-06-22T10:11:40","slug":"help-sheets","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/summer-school-materials\/help-sheets\/","title":{"rendered":"Technical help sheet"},"content":{"rendered":"\n

Introductory computational and data visualisation skills<\/h2>\n\n\n\n
Rstudio & R<\/td>https:\/\/posit.co\/products\/open-source\/rstudio\/<\/a> <\/td><\/tr>
R libraries: tidyverse, ggplot2, gProfiler2<\/td>install.packages(c(“tidyverse”, “gprofiler2”)<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

Genome variation across human populations<\/h2>\n\n\n\n
Variant Effect Predictor (either the command line script or its docker image)<\/td>https:\/\/www.ensembl.org\/info\/docs\/tools\/vep\/index.html<\/a><\/td><\/tr>
Samtools v1.12<\/td>http:\/\/www.htslib.org\/download\/<\/a><\/td><\/tr>
Bcftools v1.12<\/td>http:\/\/www.htslib.org\/download\/<\/a><\/td><\/tr>
GATK v4.2.0.0<\/td>https:\/\/github.com\/broadinstitute\/gatk\/releases<\/a><\/td><\/tr>
BWA<\/td><\/a>https:\/\/sourceforge.net\/projects\/bio-bwa\/files\/bwa-0.7.17.tar.bz2\/download<\/a><\/td><\/tr>
IGV
(The web browser version should be fine)<\/td>		<\/a>https:\/\/igv.org\/<\/a><\/td><\/tr>
VEP<\/td>https:\/\/www.ensembl.org\/info\/docs\/tools\/vep\/script\/vep_tutorial.html<\/a><\/td><\/tr>
Data for VEP<\/td>https:\/\/ftp.ensembl.org\/pub\/current_variation\/indexed_vep_cache\/<\/a>
homo_sapiens_vep_109_GRCh38.tar.gz<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

<\/p>\n\n\n\n

Modelling cell signalling pathways<\/h2>\n\n\n\n
COPASI<\/td>http:\/\/copasi.org\/<\/a><\/td><\/tr>
Jupytor Notebook with Tellurium Package installed<\/td>https:\/\/tellurium.readthedocs.io\/en\/latest\/installation.html<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

<\/p>\n\n\n\n

<\/p>\n\n\n\n

Interpreting functional information from large scale protein structure data<\/h2>\n\n\n\n
PyMol<\/td>https:\/\/pymol.org\/2\/ <\/a><\/td><\/tr>
Jupyter<\/td>https:\/\/jupyter.org\/<\/a><\/td><\/tr>
CCP4<\/td>https:\/\/www.ccp4.ac.uk\/download\/download_file.php?pkg=setup-64&os=linux&sid=ae2fafe0f387f669960cfa4fc9e7e85b0d570c7f <\/a><\/td><\/tr>
Python with packages: sys, pprint, solrq, pandas, numpy, requests, matplotlib, ipython<\/td>https:\/\/www.python.org\/<\/a><\/td><\/tr>
VSCode<\/td>https:\/\/code.visualstudio.com\/sha\/download?build=stable&os=linux-deb-x64<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

<\/p>\n\n\n\n

Networks and pathways<\/h2>\n\n\n\n
Cytoscape <\/td>https:\/\/cytoscape.org\/ <\/a> <\/td><\/tr>
Rstudio<\/td>https:\/\/www.rstudio.com\/<\/a> <\/td><\/tr>
SummarizedExperiment R package<\/td>https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/SummarizedExperiment.html<\/a><\/td><\/tr>
limma R package<\/td>https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/limma.html<\/a><\/td><\/tr>
gprofiler2<\/td>https:\/\/cran.r-project.org\/web\/packages\/gprofiler2\/index.html<\/a><\/td><\/tr>
tidyverse<\/td>https:\/\/www.tidyverse.org\/<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

Introductory computational and data visualisation skills Rstudio & R https:\/\/posit.co\/products\/open-source\/rstudio\/ R libraries: tidyverse, ggplot2, gProfiler2 install.packages(c(“tidyverse”, “gprofiler2”) Genome variation across human populations Variant Effect Predictor (either the command line script or its docker image) https:\/\/www.ensembl.org\/info\/docs\/tools\/vep\/index.html Samtools v1.12 http:\/\/www.htslib.org\/download\/ Bcftools v1.12 http:\/\/www.htslib.org\/download\/ GATK v4.2.0.0 https:\/\/github.com\/broadinstitute\/gatk\/releases BWA https:\/\/sourceforge.net\/projects\/bio-bwa\/files\/bwa-0.7.17.tar.bz2\/download IGV(The web browser version should be fine) https:\/\/igv.org\/ VEP…<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":9,"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\/summer-school-materials\/wp-json\/wp\/v2\/pages\/18","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/summer-school-materials\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/summer-school-materials\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/summer-school-materials\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/summer-school-materials\/wp-json\/wp\/v2\/comments?post=18"}],"version-history":[{"count":12,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/summer-school-materials\/wp-json\/wp\/v2\/pages\/18\/revisions"}],"predecessor-version":[{"id":1645,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/summer-school-materials\/wp-json\/wp\/v2\/pages\/18\/revisions\/1645"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/summer-school-materials\/wp-json\/wp\/v2\/media?parent=18"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}