Online documentation
This vignette displays pre-computed results. Run the targets pipeline locally for interactive analysis.
Overview
The CoMMpass Analysis project provides pre-computed analysis results as static JSON files hosted on GitHub Pages. These endpoints are updated on each pipeline run and serve read-only data derived from the GDC portal.
Base URL: https://JohnGavin.github.io/coMMpass-analysis/api/v1/
Data is pre-computed via a targets pipeline and serialized to JSON. For raw (non-derived) data, visit the original data sources listed in the Raw Data Sources section below.
Available Endpoints
The table below lists all JSON API endpoints with their descriptions and record counts.
Static API endpoints for CoMMpass analysis results. Base URL: https://JohnGavin.github.io/coMMpass-analysis/api/v1. Data is pre-computed and updated on each pipeline run.
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|
name
|
url
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description
|
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1
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clinical
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https://JohnGavin.github.io/coMMpass-analysis/api/v1/clinical.json
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Clinical data for CoMMpass patients
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2
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de-results
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https://JohnGavin.github.io/coMMpass-analysis/api/v1/de-results.json
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Differential expression results (DESeq2)
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3
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survival
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https://JohnGavin.github.io/coMMpass-analysis/api/v1/survival.json
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Prepared survival data with covariates
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|
4
|
pathways
|
https://JohnGavin.github.io/coMMpass-analysis/api/v1/pathways.json
|
GSEA pathway analysis results
|
|
5
|
cytogenetics
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https://JohnGavin.github.io/coMMpass-analysis/api/v1/cytogenetics.json
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Cytogenetic marker status and risk classification
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|
6
|
data-dictionary
|
https://JohnGavin.github.io/coMMpass-analysis/api/v1/data-dictionary.json
|
Variable metadata and data dictionary
|
Example: curl
Fetch endpoint data from the command line using curl and jq.
Show code
safe_tar_read("code_api_curl")
Fetch the endpoint index
curl -s https://JohnGavin.github.io/coMMpass-analysis/api/v1/index.json | jq .
Fetch clinical data
curl -s https://JohnGavin.github.io/coMMpass-analysis/api/v1/clinical.json | jq ‘.metadata’
Download survival data
curl -o survival.json https://JohnGavin.github.io/coMMpass-analysis/api/v1/survival.json
Example: R (jsonlite)
Load API data directly into R data frames using jsonlite::fromJSON().
Show code
safe_tar_read("code_api_r")
base_url <- “https://JohnGavin.github.io/coMMpass-analysis/api/v1”
Read endpoint index
index <- jsonlite::fromJSON(paste0(base_url, “/index.json”)) index$endpoints
Load clinical data as data frame
clinical <- jsonlite::fromJSON(paste0(base_url, “/clinical.json”)) str(clinicaldata)
Load survival data
surv <- jsonlite::fromJSON(paste0(base_url, “/survival.json”)) dim(surv$data)
Example: Python (requests)
Access the API from Python using requests and pandas.
Show code
safe_tar_read("code_api_python")
import requests import pandas as pd
base_url = “https://JohnGavin.github.io/coMMpass-analysis/api/v1”
Fetch clinical data
resp = requests.get(f”{base_url}/clinical.json”) data = resp.json() print(f”Rows: {data[‘metadata’][‘n_rows’]}“)
Convert to DataFrame
df = pd.DataFrame(data[‘data’]) print(df.head())
Raw Data Sources
This pipeline uses open-access GDC data only. For non-derived data:
Additional data (FISH, PFS, treatment response) would require MMRF Researcher Gateway access (https://research.themmrf.org/), which is not currently available to this project.
Phase 2 Roadmap
A future release will provide a dynamic plumber API with query parameters for filtering, subsetting, and custom analyses. The plumber endpoint functions already exist in R/10_api.R and inst/plumber/plumber.R. Phase 2 will add authentication, rate limiting, and OpenAPI documentation.
Data Sources
Results in this vignette are derived from the MMRF CoMMpass study (MMRF-COMMPASS, ~1,143 patients), downloaded via TCGAbiolinks. The pipeline runs with a configurable sample_limit (default 200; CI uses 20).
For full citations, data access tiers, and the distinction between pipeline data and synthetic test data, see the Data Sources vignette.
Recent Changes
Recent project commits with lines added, files changed, and change categories.
Last 20 project commits with change statistics. Date = commit date; Type = conventional-commit prefix (feat/fix/docs/ci/refactor/test/chore). Files = number of files modified; +Lines/-Lines = lines added/removed. Source: git log –numstat. See changes-by-type table for aggregate breakdown.
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date
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type
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summary
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n_files
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lines_added
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lines_removed
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file_categories
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2026-03-14
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Bug Fix
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fix(pipeline): Fix 11 NULL targets — DE condition, ID matching, consensus type
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41
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146
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47
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Other, R Source
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2026-03-14
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Bug Fix
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fix(cachix): Remove –watch-mode auto flag (already default)
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1
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1
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1
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Other
|
|
2026-03-14
|
Bug Fix
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fix(pipeline): Fix 3 NULL-target bugs, auto-generate package.nix (#93)
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87
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235
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80
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Config, Docs, Other, R Source
|
|
2026-03-14
|
Bug Fix
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fix(nix): Fix cachix signing key, rebuild Bioconductor-dependent targets
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2
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0
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0
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Other
|
|
2026-03-14
|
New Feature
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feat(captions): Add dynamic captions to 34 table/plot targets
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22
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579
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89
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Other, R Source
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2026-03-14
|
Bug Fix
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fix(vignettes): Enforce zero-computation rule — 22 violations → 0
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32
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360
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764
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Other, R Source, Vignettes
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2026-03-13
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Bug Fix
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fix(vignettes): Convert kable RDS to data.frames, fix telemetry eval guards
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18
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8
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2
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Other, Vignettes
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|
2026-03-13
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Bug Fix
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fix(ci): Save data frames (not DT widgets) to RDS for Nix portability
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3
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0
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0
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Other
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2026-03-13
|
Bug Fix
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fix(vignettes): Use Quarto #| eval syntax for pkgdown-banner chunks
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11
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44
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11
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Vignettes
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2026-03-13
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Refactoring
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refactor(targets): Move Bioconductor packages to per-target declarations
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11
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35
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17
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Other, R Source, Vignettes
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2026-03-13
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New Feature
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feat(vignettes): Add code provenance, kable→DT conversion, caption compliance
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35
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1004
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437
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CI/CD, Other, R Source, Vignettes
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2026-03-13
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Bug Fix
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fix(vignettes): Skip NULL RDS in safe_tar_read, return invisible(NULL)
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11
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22
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22
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Vignettes
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2026-03-13
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Bug Fix
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fix(glossary): Prevent double DT::datatable() wrapping in glossary-table chunk
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1
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3
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1
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Vignettes
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2026-03-13
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CI/CD
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ci: Show quarto errors with quiet=FALSE, render individual vignettes in diagnostic
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1
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20
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6
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CI/CD
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2026-03-13
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CI/CD
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ci: Add verbose quarto error diagnostics on build failure
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1
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14
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1
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CI/CD
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2026-03-13
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Bug Fix
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fix(vignettes): Strip Nix paths from DT widgets, auto-wrap data frames
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25
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66
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28
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CI/CD, Other, Vignettes
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2026-03-13
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CI/CD
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ci: Add diagnostic quarto render step to debug build failure
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1
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17
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0
|
CI/CD
|
|
2026-03-13
|
Bug Fix
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fix(vignettes): Revert safe_tar_read placeholder, guard gene-report
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11
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12
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56
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Vignettes
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|
2026-03-13
|
Maintenance
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chore: Export vig_count_distribution_plot as ggplot RDS (513KB)
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1
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0
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0
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Other
|
|
2026-03-13
|
Bug Fix
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fix(vignettes): Enable code eval in CI with RDS fallback
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80
|
113
|
74
|
CI/CD, Other, R Source, Vignettes
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Reproducibility
Session Info (click to expand)
Show code
sessionInfo()
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#> Platform: x86_64-pc-linux-gnu
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