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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| # For most projects, this workflow file will not need changing; you simply need | ||
| # to commit it to your repository. | ||
| # | ||
| # You may wish to alter this file to override the set of languages analyzed, | ||
| # or to provide custom queries or build logic. | ||
| # | ||
| # ******** NOTE ******** | ||
| # We have attempted to detect the languages in your repository. Please check | ||
| # the `language` matrix defined below to confirm you have the correct set of | ||
| # supported CodeQL languages. | ||
| # | ||
| name: "CodeQL" | ||
|
|
||
| on: | ||
| push: | ||
| branches: [ "master", production ] | ||
| pull_request: | ||
| # The branches below must be a subset of the branches above | ||
| branches: [ "master" ] | ||
| schedule: | ||
| - cron: '22 4 * * 5' | ||
|
|
||
| jobs: | ||
| analyze: | ||
| name: Analyze | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| actions: read | ||
| contents: read | ||
| security-events: write | ||
|
|
||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| language: [ 'javascript' ] | ||
| # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ] | ||
| # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support | ||
|
|
||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v3 | ||
|
|
||
| # Initializes the CodeQL tools for scanning. | ||
| - name: Initialize CodeQL | ||
| uses: github/codeql-action/init@v2 | ||
| with: | ||
| languages: ${{ matrix.language }} | ||
| # If you wish to specify custom queries, you can do so here or in a config file. | ||
| # By default, queries listed here will override any specified in a config file. | ||
| # Prefix the list here with "+" to use these queries and those in the config file. | ||
|
|
||
| # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs | ||
| # queries: security-extended,security-and-quality | ||
|
|
||
|
|
||
| # Autobuild attempts to build any compiled languages (C/C++, C#, or Java). | ||
| # If this step fails, then you should remove it and run the build manually (see below) | ||
| - name: Autobuild | ||
| uses: github/codeql-action/autobuild@v2 | ||
|
|
||
| # ℹ️ Command-line programs to run using the OS shell. | ||
| # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun | ||
|
|
||
| # If the Autobuild fails above, remove it and uncomment the following three lines. | ||
| # modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance. | ||
|
|
||
| # - run: | | ||
| # echo "Run, Build Application using script" | ||
| # ./location_of_script_within_repo/buildscript.sh | ||
|
|
||
| - name: Perform CodeQL Analysis | ||
| uses: github/codeql-action/analyze@v2 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -9,6 +9,7 @@ import { | |
| } from "@material-ui/core"; | ||
| import { useRootStyles } from "../../../rootStyles"; | ||
| import exampleScreenShot from "../../../img/example-colab-screenshot.png"; | ||
| import exampleUpsetPlot from "../../../img/example-colab-screenshot.upset.png"; | ||
|
|
||
| const CodeBasedExplorationPage: React.FC<{ | ||
| history: any; | ||
|
|
@@ -55,65 +56,98 @@ const CodeBasedExplorationPage: React.FC<{ | |
| Some data from CIDC is available for direct querying | ||
| and exploration via Google's BigQuery database | ||
| system. We provide tables of participant- and | ||
| sample-level metadata, including some clinical data. | ||
| Additionally, we are working with researchers and | ||
| statisticians to support some widely-used and | ||
| high-impact assay data tables for direct analysis | ||
| with minimal setup. | ||
| sample-level metadata. Additionally, we are working | ||
| with researchers and statisticians to figure out | ||
| some widely-used and high-impact assay data tables | ||
| for direct analysis with minimal setup. | ||
| </Typography> | ||
| <Typography> | ||
| These datasets are most easily accessed via python | ||
| notebooks hosted on Google's Colaboratory, for which | ||
| we have several examples listed below. CIDC will | ||
| allow data access for all approved users. Please | ||
| contact CIDC at{" "} | ||
| we have a few templates and examples listed below. | ||
| CIDC enables data access for all approved users. | ||
| Please contact CIDC at | ||
| <a href="mailto:[email protected]"> | ||
| [email protected] | ||
| </a>{" "} | ||
| for access to the data tables. The same data | ||
| restrictions and security apply to all data accessed | ||
| via this mechanism as via the portal. | ||
| </a> | ||
| if you have any issues accessing the data | ||
| tables. The same data restrictions and security | ||
| apply to all data accessed via this mechanism as via | ||
| the portal. | ||
| </Typography> | ||
| </CardContent> | ||
| </Card> | ||
| </Grid> | ||
| <Grid item> | ||
| <Card style={{ maxWidth: 1100, width: 1100 }}> | ||
| <CardHeader title="Examples" /> | ||
| <CardHeader title="Templates and Examples" /> | ||
| <CardContent className="markdown-body"> | ||
| <ul> | ||
| {[ | ||
| { | ||
| name: "Introductory Tutorial", | ||
| destination: null | ||
| }, | ||
| { | ||
| name: "Participant and sample exploration", | ||
| name: | ||
| "Template: Upset Plot by Trial and/or Assay", | ||
| destination: | ||
| "https://colab.research.google.com/drive/1VXVLpLE9_D7fW5cZP4j2jyTOA4q42sJk#scrollTo=R_PNmBI99t4G" | ||
| "https://colab.research.google.com/drive/14xys5GrZ7OzCC5eUYMrexM9Imq4szw7o", | ||
| description: | ||
| "a template meant for copying and modification by the user to generate their own upset plots " + | ||
| "showing the number of participants with a given subset of assays across a given subset of trials" | ||
| }, | ||
| { | ||
| name: | ||
| "Analysis of WES variants for 10021 from filtered .maf files", | ||
| "Template: Upset Plot for Collection Events on a Single Trial", | ||
| destination: | ||
| "https://colab.research.google.com/drive/11BfQsD5QgShJCGWjpnhhq6OPtUVwiPgN" | ||
| "https://colab.research.google.com/drive/1kheXUtozN6dcxdrf_U_WtnXUiDBhEMt2", | ||
| description: | ||
| "a template meant for copying and modification by the user to generate their own upset plots " + | ||
| "showing the number of participants with a given subset of collection events across a single trial" | ||
| }, | ||
| { | ||
| name: | ||
| "Analysis of RNAseq with sample metadata for 10021 from quant.sf", | ||
| "Example: Participant and Sample Exploration", | ||
| destination: | ||
| "https://colab.research.google.com/drive/1mdm4ONM0BwoBCbyGk0N2DVFEDN8Ob9Iw" | ||
| "https://colab.research.google.com/drive/1VXVLpLE9_D7fW5cZP4j2jyTOA4q42sJk", | ||
| description: | ||
| "a demonstration of more complex code-based filtering and exploration of samples and participants" | ||
| } | ||
| ].map(item => | ||
| item.destination == null ? ( | ||
| item.description == null ? ( | ||
| <li key={item.name}> | ||
| <b> | ||
| {item.name} (under construction) | ||
| </b> | ||
| </li> | ||
| ) : ( | ||
| <li key={item.name}> | ||
| <b> | ||
| {item.name} (under construction) | ||
| </b>{" "} | ||
| - {item.description} | ||
| </li> | ||
| ) | ||
| ) : item.description == null ? ( | ||
| <li key={item.name}> | ||
| {item.name} (under construction) | ||
| <a | ||
| href={item.destination} | ||
| target="_blank" | ||
| rel="noopener noreferrer" | ||
| > | ||
| {item.name} | ||
| </a> | ||
| </li> | ||
| ) : ( | ||
| <li key={item.name}> | ||
| <a href={item.destination}> | ||
| {item.name} | ||
| </a> | ||
| <b> | ||
| <a | ||
| href={item.destination} | ||
| target="_blank" | ||
| rel="noopener noreferrer" | ||
| > | ||
| {item.name} | ||
| </a> | ||
| </b>{" "} | ||
| - {item.description} | ||
| </li> | ||
| ) | ||
| )} | ||
|
|
@@ -128,7 +162,13 @@ const CodeBasedExplorationPage: React.FC<{ | |
| <img | ||
| src={exampleScreenShot} | ||
| alt={ | ||
| "Screenshot of a Kaplan-Meier curve for trial 10021. One subplot per cohort, one line per trial arm." | ||
| "Screenshot of Google Colaboratory interface for Upset Plot Template, showing the top of Section 3. Parameters where you can choose trials to include in the plot." | ||
| } | ||
| ></img> | ||
| <img | ||
| src={exampleUpsetPlot} | ||
| alt={ | ||
| "Upset plot as generated in Google Colaboratory using the Upset Plot Template." | ||
| } | ||
| ></img> | ||
| </CardContent> | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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|
@@ -38,7 +38,6 @@ const NONASSAY_FIELDS = [ | |
|
|
||
| const ASSAYS_WITH_ANALYSIS = [ | ||
| "atacseq", | ||
| "ctdna", | ||
| "cytof", | ||
| "rna", | ||
| "tcr", | ||
|
|
||
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