From 9eb5216c03c62304d1b54f719248b46d50163417 Mon Sep 17 00:00:00 2001 From: Quarto GHA Workflow Runner Date: Wed, 3 Apr 2024 14:20:21 +0000 Subject: [PATCH] Built site for gh-pages --- .nojekyll | 2 +- develop/03_DOD.html | 106 +++---- develop/examples/NGS_metadata.html | 434 +++++++++++++++-------------- develop/practical_workshop.html | 318 ++++++++++----------- people.html | 4 +- search.json | 2 +- sitemap.xml | 36 +-- 7 files changed, 452 insertions(+), 450 deletions(-) diff --git a/.nojekyll b/.nojekyll index 28382264..7d065be9 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -31ded030 \ No newline at end of file +71fdcd1f \ No newline at end of file diff --git a/develop/03_DOD.html b/develop/03_DOD.html index 2a9621bf..c26fd9cc 100644 --- a/develop/03_DOD.html +++ b/develop/03_DOD.html @@ -953,23 +953,23 @@

Naming conventions

-
- diff --git a/develop/examples/NGS_metadata.html b/develop/examples/NGS_metadata.html index ed9f0e66..99366ceb 100644 --- a/develop/examples/NGS_metadata.html +++ b/develop/examples/NGS_metadata.html @@ -253,34 +253,36 @@

NGS Assay and Project metadata

⏰ Time Estimation: X minutes

-

💬 Learning Objectives:
-1. Develop your own metadata

+

💬 Learning Objectives:

+
    +
  1. Develop your metadata
    2. +

You should consider revisiting these examples after completing lesson 4 in the course material. Please review these three tables containing pre-filled data fields for metadata, each serving distinct purposes: sample metadata, project metadata, and experimental metadata.

Sample metadata fields

-

Some details might be specific to your samples. For example, which samples are treated, which are control, which tissue they come from, which cell type, the age, etc. Here is a list of possible metadata fields that you can use:

+

Some details might be specific to your samples. For example, which samples are treated, which are controlled, which tissue they come from, which cell type, the age, etc. Here is a list of possible metadata fields that you can use:

-
- @@ -849,23 +851,23 @@

Project metadata f
-
- @@ -1343,23 +1345,23 @@

Assay metadata field
-
- @@ -1942,28 +1944,28 @@

Assay metadata field

-

It is important that the metadata includes key details such as the project’s short description, author information, creation date, experimental protocol, assay ID, assay type, platform utilized, library details, keywords, sample count, paired-end status, processor information, organism studied, sample origin, and file path.

+

The metadata must include key details such as the project’s short description, author information, creation date, experimental protocol, assay ID, assay type, platform utilized, library details, keywords, sample count, paired-end status, processor information, organism studied, sample origin, and file path.

If you would create a database from the metadata files, your table should look like this (each row corresponding to one project):

-
- diff --git a/develop/practical_workshop.html b/develop/practical_workshop.html index 5f25faca..f852be03 100644 --- a/develop/practical_workshop.html +++ b/develop/practical_workshop.html @@ -545,23 +545,23 @@

Assay metadata field
-
- @@ -1151,23 +1151,23 @@

Project metadata f
-
- @@ -1761,23 +1761,23 @@

Suggestions for N
-
- diff --git a/people.html b/people.html index 261314e7..051ba951 100644 --- a/people.html +++ b/people.html @@ -223,7 +223,7 @@

People

-
+

@@ -245,7 +245,7 @@

-
+

diff --git a/search.json b/search.json index 4effa689..01b7795e 100644 --- a/search.json +++ b/search.json @@ -159,7 +159,7 @@ "href": "develop/examples/NGS_metadata.html", "title": "NGS Assay and Project metadata", "section": "", - "text": "Section Overview\n\n\n\n⏰ Time Estimation: X minutes\n💬 Learning Objectives:\n1. Develop your own metadata\n\n\nYou should consider revisiting these examples after completing lesson 4 in the course material. Please review these three tables containing pre-filled data fields for metadata, each serving distinct purposes: sample metadata, project metadata, and experimental metadata.\n\nSample metadata fields\nSome details might be specific to your samples. For example, which samples are treated, which are control, which tissue they come from, which cell type, the age, etc. Here is a list of possible metadata fields that you can use:\n\n\n\n\n\n\n\n\n\nMetadata field\nDefinition\nFormat\nOntology\nExample\n\n\n\n\nsample\nName of the sample\nNA\nNA\ncontrol_rep1, treat_rep1\n\n\nfastq_1\nPath to fastq file 1\nNA\nNA\nAEG588A1_S1_L002_R1_001.fastq.gz\n\n\nfastq_2\nPath to paired fastq file, if it is a paired experiment\nNA\nNA\nAEG588A1_S1_L002_R2_001.fastq.gz\n\n\nstrandedness\nThe strandedness of the cDNA library\n<unstranded OR forward OR reverse \\>\nNA\nunstranded\n\n\ncondition\nVariable of interest of the experiment, such as \"control\", \"treatment\", etc\nwordWord\ncamelCase\ncontrol, treat1, treat2\n\n\ncell_type\nThe cell type(s) known or selected to be present in the sample\nNA\nontology field- e.g. EFO or OBI\nNA\n\n\ntissue\nThe tissue from which the sample was taken\nNA\nUberon\nNA\n\n\nsex\nThe biological/genetic sex of the sample\nNA\nontology field- e.g. EFO or OBI\nNA\n\n\ncell_line\nCell line of the sample\nNA\nontology field- e.g. EFO or OBI\nNA\n\n\norganism\nOrganism origin of the sample\n<Genus species>\nTaxonomy\nMus musculus\n\n\nreplicate\nReplicate number\n<integer\\>\nNA\n1\n\n\nbatch\nBatch information\nwordWord\ncamelCase\n1\n\n\ndisease\nAny diseases that may affect the sample\nNA\nDisease Ontology or MONDO\nNA\n\n\ndevelopmental_stage\nThe developmental stage of the sample\nNA\nNA\nNA\n\n\nsample_type\nThe type of the collected specimen, eg tissue biopsy, blood draw or throat swab\nNA\nNA\nNA\n\n\nstrain\nStrain of the species from which the sample was collected, if applicable\nNA\nontology field - e.g. NCBITaxonomy\nNA\n\n\ngenetic variation\nAny relevant genetic differences from the specimen or sample to the expected genomic information for this species, eg abnormal chromosome counts, major translocations or indels\nNA\nNA\nNA\n\n\n\n\n\n\n\n\n\n\nProject metadata fields\nHere you will find a table with possible metadata fields that you can use to annotate and track your Project folders:\n\n\n\n\n\n\n\n\n\nMetadata field\nDefinition\nFormat\nOntology\nExample\n\n\n\n\nproject\nProject ID\n<surname\\>_et_al_2023\nNA\nproks_et_al_2023\n\n\nauthor\nOwner of the project\n<First name\\> <Surname\\>\nNA\nMartin Proks\n\n\ndate\nDate of creation\nYYYYMMDD\nNA\n20230101\n\n\ndescription\nShort description of the project\nPlain text\nNA\nThis is a project describing the effect of Oct4 perturbation after pERK activation\n\n\n\n\n\n\n\n\n\n\nAssay metadata fields\nHere you will find a table with possible metadata fields that you can use to annotate and track your Assay folders:\n\n\n\n\n\n\n\n\n\nMetadata field\nDefinition\nFormat\nOntology\nExample\n\n\n\n\nassay_ID\nIdentifier for the assay that is at least unique within the project\n<Assay-ID\\>_<keyword\\>_YYYYMMDD\nNA\nCHIP_Oct4_20200101\n\n\nassay_type\nThe type of experiment performed, eg ATAC-seq or seqFISH\nNA\nontology field- e.g. EFO or OBI\nChIPseq\n\n\nassay_subtype\nMore specific type or assay like bulk nascent RNAseq or single cell ATACseq\nNA\nontology field- e.g. EFO or OBI\nbulk ChIPseq\n\n\nowner\nOwner of the assay (who made the experiment?).\n<First Name\\> <Last Name\\>\nNA\nJose Romero\n\n\nplatform\nThe type of instrument used to perform the assay, eg Illumina HiSeq 4000 or Fluidigm C1 microfluidics platform\nNA\nontology field- e.g. EFO or OBI\nIllumina\n\n\nextraction_method\nTechnique used to extract the nucleic acid from the cell\nNA\nontology field- e.g. EFO or OBI\nNA\n\n\nlibrary_method\nTechnique used to amplify a cDNA library\nNA\nontology field- e.g. EFO or OBI\nNA\n\n\nexternal_accessions\nAccession numbers from external resources to which assay or protocol information was submitted\nNA\neg protocols.io, AE, GEO accession number, etc\nGSEXXXXX\n\n\nkeyword\nKeyword for easy identification\nwordWord\ncamelCase\nOct4ChIP\n\n\ndate\nDate of assay creation\nYYYYMMDD\nNA\n20200101\n\n\nnsamples\nNumber of samples analyzed in this assay\n<integer\\>\nNA\n9\n\n\nis_paired\nPaired fastq files or not\n<single OR paired\\>\nNA\nsingle\n\n\npipeline\nPipeline used to process data and version\nNA\nNA\nnf-core/chipseq -r 1.0\n\n\nstrandedness\nThe strandedness of the cDNA library\n<+ OR - OR *\\>\nNA\n*\n\n\nprocessed_by\nWho processed the data\n<First Name\\> <Last Name\\>\nNA\nSarah Lundregan\n\n\norganism\nOrganism origin\n<Genus species\\>\nTaxonomy name\nMus musculus\n\n\norigin\nIs internal or external (from a public resources) data\n<internal OR external\\>\nNA\ninternal\n\n\npath\nPath to files\n</path/to/file\\>\nNA\nNA\n\n\nshort_desc\nShort description of the assay\nplain text\nNA\nOct4 ChIP after pERK activation\n\n\nELN_ID\nID of the experiment/assay in your Electronic Lab Notebook software, like labguru or benchling\nplain text\nNA\nNA\n\n\n\n\n\n\n\n\nIt is important that the metadata includes key details such as the project’s short description, author information, creation date, experimental protocol, assay ID, assay type, platform utilized, library details, keywords, sample count, paired-end status, processor information, organism studied, sample origin, and file path.\nIf you would create a database from the metadata files, your table should look like this (each row corresponding to one project):\n\n\n\n\n\n\n\n\n\nassay_ID\nassay_type\nassay_subtype\nowner\nplatform\nextraction_method\nlibrary_method\nexternal_accessions\nkeyword\ndate\nnsamples\nis_paired\npipeline\nstrandedness\nprocessed_by\norganism\norigin\npath\nshort_desc\nELN_ID\n\n\n\n\nRNA_oct4_20200101\nRNAseq\nbulk RNAseq\nSarah Lundregan\nNextSeq 2000\nNA\nNA\nNA\noct4\n20200101\n9\npaired\nnf-core/chipseq 2.3.1\n*\nSL\nMus musculus\ninternal\nNA\nBulk RNAseq of Oct4 knockout\n234\n\n\nCHIP_oct4_20200101\nChIPseq\nbulk ChIPseq\nJose Romero\nNextSeq 2000\nNA\nNA\nNA\noct4\n20200101\n9\nsingle\nnf-core/rnaseq 3.12.0\n*\nJARH\nMus musculus\ninternal\nNA\nBulk ChIPseq of Oct4 overexpression\n123\n\n\nCHIP_med1_20190204\nChIPseq\nbulk ChIPseq\nMartin Proks\nNextSeq 2000\nNA\nNA\nNA\nmed1\n20190204\n12\nsingle\nnf-core/rnaseq 3.12.0\n*\nMP\nMus musculus\ninternal\nNA\nBulk ChIPseq of Med1 overexpression\n345\n\n\nSCR_humanSkin_20210302\nRNAseq\nsingle cell RNAseq\nJose Romero\nNextSeq 2000\nNA\nNA\nNA\nhumanSkin\n20210302\n23123\npaired\nnf-core/scrnaseq 1.8.2\n*\nJARH\nHomo sapiens\nexternal\nNA\nscRNAseq analysis of human skin development\nNA\n\n\nSCR_humanBrain_20220610\nRNAseq\nsingle cell RNAseq\nMartin Proks\nNextSeq 2000\nNA\nNA\nNA\nhumanBrain\n20220610\n1234\npaired\ncustom\n*\nMP\nHomo sapiens\nexternal\nNA\nscRNAseq analysis of human brain development\nNA\n\n\n\n\n\n\n\n\n\n\n\n\nCopyrightCC-BY-SA 4.0 license", + "text": "Section Overview\n\n\n\n⏰ Time Estimation: X minutes\n💬 Learning Objectives:\n\nDevelop your metadata\n\n\n\nYou should consider revisiting these examples after completing lesson 4 in the course material. Please review these three tables containing pre-filled data fields for metadata, each serving distinct purposes: sample metadata, project metadata, and experimental metadata.\n\nSample metadata fields\nSome details might be specific to your samples. For example, which samples are treated, which are controlled, which tissue they come from, which cell type, the age, etc. Here is a list of possible metadata fields that you can use:\n\n\n\n\n\n\n\n\n\nMetadata field\nDefinition\nFormat\nOntology\nExample\n\n\n\n\nsample\nName of the sample\nNA\nNA\ncontrol_rep1, treat_rep1\n\n\nfastq_1\nPath to fastq file 1\nNA\nNA\nAEG588A1_S1_L002_R1_001.fastq.gz\n\n\nfastq_2\nPath to paired fastq file, if it is a paired experiment\nNA\nNA\nAEG588A1_S1_L002_R2_001.fastq.gz\n\n\nstrandedness\nThe strandedness of the cDNA library\n<unstranded OR forward OR reverse \\>\nNA\nunstranded\n\n\ncondition\nVariable of interest of the experiment, such as \"control\", \"treatment\", etc\nwordWord\ncamelCase\ncontrol, treat1, treat2\n\n\ncell_type\nThe cell type(s) known or selected to be present in the sample\nNA\nontology field- e.g. EFO or OBI\nNA\n\n\ntissue\nThe tissue from which the sample was taken\nNA\nUberon\nNA\n\n\nsex\nThe biological/genetic sex of the sample\nNA\nontology field- e.g. EFO or OBI\nNA\n\n\ncell_line\nCell line of the sample\nNA\nontology field- e.g. EFO or OBI\nNA\n\n\norganism\nOrganism origin of the sample\n<Genus species>\nTaxonomy\nMus musculus\n\n\nreplicate\nReplicate number\n<integer\\>\nNA\n1\n\n\nbatch\nBatch information\nwordWord\ncamelCase\n1\n\n\ndisease\nAny diseases that may affect the sample\nNA\nDisease Ontology or MONDO\nNA\n\n\ndevelopmental_stage\nThe developmental stage of the sample\nNA\nNA\nNA\n\n\nsample_type\nThe type of the collected specimen, eg tissue biopsy, blood draw or throat swab\nNA\nNA\nNA\n\n\nstrain\nStrain of the species from which the sample was collected, if applicable\nNA\nontology field - e.g. NCBITaxonomy\nNA\n\n\ngenetic variation\nAny relevant genetic differences from the specimen or sample to the expected genomic information for this species, eg abnormal chromosome counts, major translocations or indels\nNA\nNA\nNA\n\n\n\n\n\n\n\n\n\n\nProject metadata fields\nHere you will find a table with possible metadata fields that you can use to annotate and track your Project folders:\n\n\n\n\n\n\n\n\n\nMetadata field\nDefinition\nFormat\nOntology\nExample\n\n\n\n\nproject\nProject ID\n<surname\\>_et_al_2023\nNA\nproks_et_al_2023\n\n\nauthor\nOwner of the project\n<First name\\> <Surname\\>\nNA\nMartin Proks\n\n\ndate\nDate of creation\nYYYYMMDD\nNA\n20230101\n\n\ndescription\nShort description of the project\nPlain text\nNA\nThis is a project describing the effect of Oct4 perturbation after pERK activation\n\n\n\n\n\n\n\n\n\n\nAssay metadata fields\nHere you will find a table with possible metadata fields that you can use to annotate and track your Assay folders:\n\n\n\n\n\n\n\n\n\nMetadata field\nDefinition\nFormat\nOntology\nExample\n\n\n\n\nassay_ID\nIdentifier for the assay that is at least unique within the project\n<Assay-ID\\>_<keyword\\>_YYYYMMDD\nNA\nCHIP_Oct4_20200101\n\n\nassay_type\nThe type of experiment performed, eg ATAC-seq or seqFISH\nNA\nontology field- e.g. EFO or OBI\nChIPseq\n\n\nassay_subtype\nMore specific type or assay like bulk nascent RNAseq or single cell ATACseq\nNA\nontology field- e.g. EFO or OBI\nbulk ChIPseq\n\n\nowner\nOwner of the assay (who made the experiment?).\n<First Name\\> <Last Name\\>\nNA\nJose Romero\n\n\nplatform\nThe type of instrument used to perform the assay, eg Illumina HiSeq 4000 or Fluidigm C1 microfluidics platform\nNA\nontology field- e.g. EFO or OBI\nIllumina\n\n\nextraction_method\nTechnique used to extract the nucleic acid from the cell\nNA\nontology field- e.g. EFO or OBI\nNA\n\n\nlibrary_method\nTechnique used to amplify a cDNA library\nNA\nontology field- e.g. EFO or OBI\nNA\n\n\nexternal_accessions\nAccession numbers from external resources to which assay or protocol information was submitted\nNA\neg protocols.io, AE, GEO accession number, etc\nGSEXXXXX\n\n\nkeyword\nKeyword for easy identification\nwordWord\ncamelCase\nOct4ChIP\n\n\ndate\nDate of assay creation\nYYYYMMDD\nNA\n20200101\n\n\nnsamples\nNumber of samples analyzed in this assay\n<integer\\>\nNA\n9\n\n\nis_paired\nPaired fastq files or not\n<single OR paired\\>\nNA\nsingle\n\n\npipeline\nPipeline used to process data and version\nNA\nNA\nnf-core/chipseq -r 1.0\n\n\nstrandedness\nThe strandedness of the cDNA library\n<+ OR - OR *\\>\nNA\n*\n\n\nprocessed_by\nWho processed the data\n<First Name\\> <Last Name\\>\nNA\nSarah Lundregan\n\n\norganism\nOrganism origin\n<Genus species\\>\nTaxonomy name\nMus musculus\n\n\norigin\nIs internal or external (from a public resources) data\n<internal OR external\\>\nNA\ninternal\n\n\npath\nPath to files\n</path/to/file\\>\nNA\nNA\n\n\nshort_desc\nShort description of the assay\nplain text\nNA\nOct4 ChIP after pERK activation\n\n\nELN_ID\nID of the experiment/assay in your Electronic Lab Notebook software, like labguru or benchling\nplain text\nNA\nNA\n\n\n\n\n\n\n\n\nThe metadata must include key details such as the project’s short description, author information, creation date, experimental protocol, assay ID, assay type, platform utilized, library details, keywords, sample count, paired-end status, processor information, organism studied, sample origin, and file path.\nIf you would create a database from the metadata files, your table should look like this (each row corresponding to one project):\n\n\n\n\n\n\n\n\n\nassay_ID\nassay_type\nassay_subtype\nowner\nplatform\nextraction_method\nlibrary_method\nexternal_accessions\nkeyword\ndate\nnsamples\nis_paired\npipeline\nstrandedness\nprocessed_by\norganism\norigin\npath\nshort_desc\nELN_ID\n\n\n\n\nRNA_oct4_20200101\nRNAseq\nbulk RNAseq\nSarah Lundregan\nNextSeq 2000\nNA\nNA\nNA\noct4\n20200101\n9\npaired\nnf-core/chipseq 2.3.1\n*\nSL\nMus musculus\ninternal\nNA\nBulk RNAseq of Oct4 knockout\n234\n\n\nCHIP_oct4_20200101\nChIPseq\nbulk ChIPseq\nJose Romero\nNextSeq 2000\nNA\nNA\nNA\noct4\n20200101\n9\nsingle\nnf-core/rnaseq 3.12.0\n*\nJARH\nMus musculus\ninternal\nNA\nBulk ChIPseq of Oct4 overexpression\n123\n\n\nCHIP_med1_20190204\nChIPseq\nbulk ChIPseq\nMartin Proks\nNextSeq 2000\nNA\nNA\nNA\nmed1\n20190204\n12\nsingle\nnf-core/rnaseq 3.12.0\n*\nMP\nMus musculus\ninternal\nNA\nBulk ChIPseq of Med1 overexpression\n345\n\n\nSCR_humanSkin_20210302\nRNAseq\nsingle cell RNAseq\nJose Romero\nNextSeq 2000\nNA\nNA\nNA\nhumanSkin\n20210302\n23123\npaired\nnf-core/scrnaseq 1.8.2\n*\nJARH\nHomo sapiens\nexternal\nNA\nscRNAseq analysis of human skin development\nNA\n\n\nSCR_humanBrain_20220610\nRNAseq\nsingle cell RNAseq\nMartin Proks\nNextSeq 2000\nNA\nNA\nNA\nhumanBrain\n20220610\n1234\npaired\ncustom\n*\nMP\nHomo sapiens\nexternal\nNA\nscRNAseq analysis of human brain development\nNA\n\n\n\n\n\n\n\n\n\n\n\n\nCopyrightCC-BY-SA 4.0 license", "crumbs": [ "Use cases", "NGS data", diff --git a/sitemap.xml b/sitemap.xml index de86033a..df938948 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -2,74 +2,74 @@ https://hds-sandbox.github.io/RDM_NGS_course/index.html - 2024-04-03T14:18:04.114Z + 2024-04-03T14:18:46.464Z https://hds-sandbox.github.io/RDM_NGS_course/cards/AlbaMartinez.html - 2024-04-03T14:18:04.070Z + 2024-04-03T14:18:46.420Z https://hds-sandbox.github.io/RDM_NGS_course/people.html - 2024-04-03T14:18:04.114Z + 2024-04-03T14:18:46.464Z https://hds-sandbox.github.io/RDM_NGS_course/develop/contributors.html - 2024-04-03T14:18:04.086Z + 2024-04-03T14:18:46.440Z https://hds-sandbox.github.io/RDM_NGS_course/develop/06_pipelines.html - 2024-04-03T14:18:04.070Z + 2024-04-03T14:18:46.420Z https://hds-sandbox.github.io/RDM_NGS_course/develop/05_VC.html - 2024-04-03T14:18:04.070Z + 2024-04-03T14:18:46.420Z https://hds-sandbox.github.io/RDM_NGS_course/develop/07_repos.html - 2024-04-03T14:18:04.070Z + 2024-04-03T14:18:46.420Z https://hds-sandbox.github.io/RDM_NGS_course/develop/examples/NGS_metadata.html - 2024-04-03T14:18:04.086Z + 2024-04-03T14:18:46.440Z https://hds-sandbox.github.io/RDM_NGS_course/develop/01_RDM_intro.html - 2024-04-03T14:18:04.070Z + 2024-04-03T14:18:46.420Z https://hds-sandbox.github.io/RDM_NGS_course/develop/02_DMP.html - 2024-04-03T14:18:04.070Z + 2024-04-03T14:18:46.420Z https://hds-sandbox.github.io/RDM_NGS_course/develop/examples/NGS_management.html - 2024-04-03T14:18:04.086Z + 2024-04-03T14:18:46.440Z https://hds-sandbox.github.io/RDM_NGS_course/develop/examples/NGS_OS_FAIR.html - 2024-04-03T14:18:04.086Z + 2024-04-03T14:18:46.440Z https://hds-sandbox.github.io/RDM_NGS_course/develop/04_metadata.html - 2024-04-03T14:18:04.070Z + 2024-04-03T14:18:46.420Z https://hds-sandbox.github.io/RDM_NGS_course/develop/03_DOD.html - 2024-04-03T14:18:04.070Z + 2024-04-03T14:18:46.420Z https://hds-sandbox.github.io/RDM_NGS_course/develop/practical_workshop.html - 2024-04-03T14:18:04.114Z + 2024-04-03T14:18:46.464Z https://hds-sandbox.github.io/RDM_NGS_course/practical_workflows.html - 2024-04-03T14:18:04.114Z + 2024-04-03T14:18:46.464Z https://hds-sandbox.github.io/RDM_NGS_course/cards/JARomero.html - 2024-04-03T14:18:04.070Z + 2024-04-03T14:18:46.420Z https://hds-sandbox.github.io/RDM_NGS_course/use_cases.html - 2024-04-03T14:18:04.114Z + 2024-04-03T14:18:46.464Z