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IGVF-3530-differential-expression #2165

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2 changes: 1 addition & 1 deletion src/igvfd/schemas/analysis_step.json
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Expand Up @@ -42,7 +42,7 @@
},
"properties": {
"schema_version": {
"default": "15"
"default": "16"
},
"analysis_step_types": {
"title": "Analysis Step Types",
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15 changes: 15 additions & 0 deletions src/igvfd/schemas/changelogs/analysis_step.md
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@@ -1,5 +1,20 @@
## Changelog for *`analysis_step.json`*

### Schema version 16

* Adjust `input_content_types` enum list to replace `global differential expression` with `global differential expression per element`.
* Adjust `output_content_types` enum list to replace `global differential expression` with `global differential expression per element`.
* Adjust `input_content_types` enum list to replace `local differential expression` with `global differential expression per element`.
* Adjust `output_content_types` enum list to replace `local differential expression` with `global differential expression per element`.
* Adjust `input_content_types` enum list to replace `cis differential expression quantifications per guide` with `local differential expression per guide`.
* Adjust `output_content_types` enum list to replace `cis differential expression quantifications per guide` with `local differential expression per guide`.
* Adjust `input_content_types` enum list to replace `trans differential expression quantifications per guide` with `global differential expression per guide`.
* Adjust `output_content_types` enum list to replace `trans differential expression quantifications per guide` with `global differential expression per guide`.
* Adjust `input_content_types` enum list to replace `cis differential expression quantifications per element` with `local differential expression per element`.
* Adjust `output_content_types` enum list to replace `cis differential expression quantifications per element` with `local differential expression per element`.
* Adjust `input_content_types` enum list to replace `trans differential expression quantifications per element` with `global differential expression per element`.
* Adjust `output_content_types` enum list to replace `trans differential expression quantifications per element` with `global differential expression per element`.

### Minor changes since schema version 15

* Extend `analysis_step_type` enum list to include `quality metrics calculation`.
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9 changes: 9 additions & 0 deletions src/igvfd/schemas/changelogs/tabular_file.md
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@@ -1,5 +1,14 @@
## Changelog for *`tabular_file.json`*

### Schema version 26

* Adjust `content_type` enum list to replace `global differential expression` with `global differential expression per element`.
* Adjust `content_type` enum list to replace `local differential expression` with `global differential expression per element`.
* Adjust `content_type` enum list to replace `cis differential expression quantifications per guide` with `local differential expression per guide`.
* Adjust `content_type` enum list to replace `trans differential expression quantifications per guide` with `global differential expression per guide`.
* Adjust `content_type` enum list to replace `cis differential expression quantifications per element` with `local differential expression per element`.
* Adjust `content_type` enum list to replace `trans differential expression quantifications per element` with `global differential expression per element`.

### Minor changes since schema version 25

* Extend `catalog_collections` enum list to include `genomic_elements_phenotypes`.
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32 changes: 13 additions & 19 deletions src/igvfd/schemas/tabular_file.json
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Expand Up @@ -159,8 +159,6 @@
"co-localization scores",
"coding variant effects",
"differential chromatin contact quantifications",
"cis differential expression quantifications per element",
"cis differential expression quantifications per guide",
"differential element quantifications",
"differential open reading frame quantifications",
"differential gene expression quantifications",
Expand All @@ -184,11 +182,13 @@
"gene programs",
"gene program regulators",
"gene universe",
"global differential expression",
"global differential expression per element",
"global differential expression per guide",
"guide quantifications",
"guide RNA sequences",
"guide RNA sequences reference",
"local differential expression",
"local differential expression per element",
"local differential expression per guide",
"loci",
"methylation counts",
"minus strand modification state",
Expand Down Expand Up @@ -219,8 +219,6 @@
"reporter variants",
"spliceQTL",
"target transcripts",
"trans differential expression quantifications per element",
"trans differential expression quantifications per guide",
"transcript quantifications",
"variant binding effects",
"variant effects",
Expand Down Expand Up @@ -319,7 +317,7 @@
"type": "object",
"properties": {
"schema_version": {
"default": "25"
"default": "26"
},
"catalog_adapters": {
"title": "IGVF Catalog Adapters",
Expand Down Expand Up @@ -362,8 +360,6 @@
"cell annotations",
"cell hashing barcodes",
"chromatin contact quantifications",
"cis differential expression quantifications per element",
"cis differential expression quantifications per guide",
"cis-trans regulatory differences",
"co-localization scores",
"coding variant effects",
Expand Down Expand Up @@ -395,13 +391,15 @@
"gene program regulators",
"gene quantifications",
"gene universe",
"global differential expression",
"global differential expression per element",
"global differential expression per guide",
"guide quantifications",
"guide RNA sequences",
"heritability enrichment",
"index plate",
"individual cells profile",
"local differential expression",
"local differential expression per element",
"local differential expression per guide",
"loci",
"machine learning model features",
"marker genes",
Expand Down Expand Up @@ -452,8 +450,6 @@
"spatial transcriptomics slide-level transcripts",
"spliceQTL",
"target transcripts",
"trans differential expression quantifications per element",
"trans differential expression quantifications per guide",
"tissue positions",
"transcript quantifications",
"variants",
Expand Down Expand Up @@ -486,8 +482,6 @@
"cell annotations": "A file containing cell classifications and/or labels based on their unique transcriptome and genomic signatures, usually generated from single cell sequencing experiments.",
"cell hashing barcodes": "The barcodes used for cell hashing.",
"chromatin contact quantifications": "A file containing chromatin conformation contacts.",
"cis differential expression quantifications per element": "Element-level differential expression results aggregated across guides targeting each element for nearby genes within a configured interval.",
"cis differential expression quantifications per guide": "Guide-level differential expression results for nearby genes within a configured interval around the guide target.",
"cis-trans regulatory differences": "Classification by gene for type of cis- or trans-acting regulation.",
"co-localization scores": "eQTL-GWAS co-localization p-values",
"coding variant effects": "A file predicting effects of amino acid changes at each position of a given protein.",
Expand Down Expand Up @@ -515,13 +509,15 @@
"gene program regulators": "Predicted regulators of a gene program.",
"gene quantifications": "The quantified levels of genes.",
"gene universe": "List of gene Ensembl ID and symbol using official IGVF GENCODE version (V43), used for downstream analysis of gene networks by the Cellular Program Networks WG.",
"global differential expression": "A file listing differentially expressed genes across the entire dataset.",
"global differential expression per element": "Element-level differential expression results aggregated across guides targeting each element across the full gene annotation.",
"global differential expression per guide": "Guide-level differential expression results across the full gene annotation.",
"guide quantifications": "Information and sequencing read counts for each gRNA in a pooled CRISPR screen experiment.",
"guide RNA sequences": "The sequences of guide RNAs designed for genome editing using CRISPR. Formatting should follow https://github.com/IGVF-DACC/checkfiles/blob/dev/src/schemas/table_schemas/guide_rna_sequences.json.",
"heritability enrichment": "A file with enrichment scores identifying if genomic annotations contribute disproportionately to the heritability of a trait.",
"index plate": "Describes the plate layout of sample index combinations (e.g., i7/i5) used for multiplexed sequencing libraries.",
"individual cells profile": "CSV file with morphological feature measurements for each imaged cell.",
"local differential expression": "A file listing differentially expressed genes within a defined genomic region surrounding a perturbation.",
"local differential expression per element": "Element-level differential expression results aggregated across guides targeting each element for nearby genes within a configured interval.",
"local differential expression per guide": "Guide-level differential expression results for nearby genes within a configured interval around the guide target.",
"loci": "A table listing genomic loci.",
"external source data": "File containing a list of urls used as a source.",
"exon constraint": "A file containing model estimates for the probability that a variant observed in the population is missense within an exon.",
Expand Down Expand Up @@ -578,8 +574,6 @@
"target transcripts": "A GTF file containing annotations of targeted transcripts by the TAP-seq primer panel.",
"tissue positions": "The spatial coordinates or positions of tissue samples or sections in experiments.",
"transcript quantifications": "The quantified levels of transcripts.",
"trans differential expression quantifications per guide": "Guide-level differential expression results across the full gene annotation.",
"trans differential expression quantifications per element": "Element-level differential expression results aggregated across guides targeting each element across the full gene annotation.",
"variants": "A table listing genetic variants, which may be called from IGVF data or collected from external resources.",
"variant binding effects": "The genetic variant effects on transcription factor binding affinity.",
"variant effects": "The genetic variant effects on gene expression.",
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12 changes: 6 additions & 6 deletions src/igvfd/tests/data/inserts/analysis_step.json
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Expand Up @@ -153,7 +153,7 @@
],
"output_content_types": [
"variant effects",
"global differential expression"
"global differential expression per element"
]
},
{
Expand Down Expand Up @@ -218,7 +218,7 @@
"reads",
"index",
"variant to cluster mapping",
"global differential expression"
"global differential expression per element"
],
"output_content_types": [
"fragments",
Expand Down Expand Up @@ -280,10 +280,10 @@
"elements reference"
],
"output_content_types": [
"cis differential expression quantifications per guide",
"trans differential expression quantifications per guide",
"cis differential expression quantifications per element",
"trans differential expression quantifications per element",
"local differential expression per guide",
"global differential expression per guide",
"local differential expression per element",
"global differential expression per element",
"pipeline dashboard"
]
}
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26 changes: 13 additions & 13 deletions src/igvfd/tests/data/inserts/tabular_file.json
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Expand Up @@ -1290,7 +1290,7 @@
],
"md5sum": "85d68e982987441946768df28b8e9af4",
"file_format": "tsv",
"content_type": "global differential expression",
"content_type": "global differential expression per element",
"reference_files": [
"IGVFFI0001GNRF"
],
Expand Down Expand Up @@ -1891,17 +1891,17 @@
"lab": "danwei-huangfu",
"award": "1U01HG012051-01",
"aliases": [
"igvf:tabular_file_cis_differential_expression_per_guide"
"igvf:tabular_file_local_differential_expression_per_guide"
],
"status": "released",
"release_timestamp": "2026-05-27T12:34:56Z",
"md5sum": "4f4f16496f0f4ee0df909bbf0d0c4c69",
"file_format": "tsv",
"content_type": "cis differential expression quantifications per guide",
"content_type": "local differential expression per guide",
"reference_files": [
"IGVFFI0001GNRF"
],
"submitted_file_name": "/Users/igvf/igvf_files/cis_differential_expression_quantifications_per_guide.tsv.gz",
"submitted_file_name": "/Users/igvf/igvf_files/local_differential_expression_per_guide.tsv.gz",
"file_size": 5310,
"upload_status": "validated",
"filtered": false,
Expand All @@ -1914,17 +1914,17 @@
"lab": "danwei-huangfu",
"award": "1U01HG012051-01",
"aliases": [
"igvf:tabular_file_trans_differential_expression_per_guide"
"igvf:tabular_file_global_differential_expression_per_guide"
],
"status": "released",
"release_timestamp": "2026-05-27T12:34:56Z",
"md5sum": "5a5f16496f0f4ee0df909bbf0d0c4c70",
"file_format": "tsv",
"content_type": "trans differential expression quantifications per guide",
"content_type": "global differential expression per guide",
"reference_files": [
"IGVFFI0001GNRF"
],
"submitted_file_name": "/Users/igvf/igvf_files/trans_differential_expression_quantifications_per_guide.tsv.gz",
"submitted_file_name": "/Users/igvf/igvf_files/global_differential_expression_per_guide.tsv.gz",
"file_size": 6520,
"upload_status": "validated",
"filtered": false,
Expand All @@ -1937,17 +1937,17 @@
"lab": "danwei-huangfu",
"award": "1U01HG012051-01",
"aliases": [
"igvf:tabular_file_cis_differential_expression_per_element"
"igvf:tabular_file_local_differential_expression_per_element"
],
"status": "released",
"release_timestamp": "2026-05-27T12:34:56Z",
"md5sum": "6b6f16496f0f4ee0df909bbf0d0c4c71",
"file_format": "tsv",
"content_type": "cis differential expression quantifications per element",
"content_type": "local differential expression per element",
"reference_files": [
"IGVFFI0001GNRF"
],
"submitted_file_name": "/Users/igvf/igvf_files/cis_differential_expression_quantifications_per_element.tsv.gz",
"submitted_file_name": "/Users/igvf/igvf_files/local_differential_expression_per_element.tsv.gz",
"file_size": 7180,
"upload_status": "validated",
"filtered": false,
Expand All @@ -1960,17 +1960,17 @@
"lab": "danwei-huangfu",
"award": "1U01HG012051-01",
"aliases": [
"igvf:tabular_file_trans_differential_expression_per_element"
"igvf:tabular_file_global_differential_expression_per_element"
],
"status": "released",
"release_timestamp": "2026-05-27T12:34:56Z",
"md5sum": "7c7f16496f0f4ee0df909bbf0d0c4c72",
"file_format": "tsv",
"content_type": "trans differential expression quantifications per element",
"content_type": "global differential expression per element",
"reference_files": [
"IGVFFI0001GNRF"
],
"submitted_file_name": "/Users/igvf/igvf_files/trans_differential_expression_quantifications_per_element.tsv.gz",
"submitted_file_name": "/Users/igvf/igvf_files/global_differential_expression_per_element.tsv.gz",
"file_size": 7395,
"upload_status": "validated",
"filtered": false,
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27 changes: 27 additions & 0 deletions src/igvfd/tests/fixtures/schemas/analysis_step.py
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Expand Up @@ -187,3 +187,30 @@ def analysis_step_v14(testapp, base_workflow):
'analysis_step_types': ['quantification']
}
return item


@pytest.fixture
def analysis_step_v15(testapp, base_workflow):
item = {
'schema_version': '15',
'step_label': 'differential-expression-analysis-step',
'title': 'Differential Expression Analysis Step',
'input_content_types': [
'global differential expression',
'local differential expression',
'cis differential expression quantifications per guide',
'trans differential expression quantifications per guide',
'cis differential expression quantifications per element',
'trans differential expression quantifications per element',
],
'output_content_types': [
'global differential expression',
'local differential expression',
'cis differential expression quantifications per guide',
'trans differential expression quantifications per guide',
'cis differential expression quantifications per element',
'trans differential expression quantifications per element',
],
'analysis_step_types': ['differential expression analysis']
}
return item
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