splicing-quantification

Name: splicing-quantification
Author: GPTomics

1.1kstars185forks

How to install splicing-quantification?

gptomics/bioskills/splicing-quantification

$npx -y skills add GPTomics/bioSkills --skill splicing-quantification

Installs into the current project.

Summary

Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-

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SKILL.md

1	## Version Compatibility
2
3	Reference examples tested with: rMATS-turbo 4.3+, SUPPA2 2.4+, leafcutter 0.2.9+, MAJIQ 3.0+, IRFinder-S 2.0+, kallisto 0.50+, Salmon 1.10+, pandas 2.2+, STAR 2.7.11+
4
5	Before using code patterns, verify installed versions match. If versions differ:
6	- Python: `pip show <package>` then `help(module.function)` to check signatures
7	- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
8	- CLI: `<tool> --version` then `<tool> --help` to confirm flags
9
10	If code throws ImportError, AttributeError, or TypeError, introspect the installed
11	package and adapt the example to match the actual API rather than retrying.
12
13	# Splicing Quantification
14
15	Quantify alternative splicing events as PSI (percent spliced in) from RNA-seq. PSI = inclusion read evidence / (inclusion + skipping read evidence), normalized for differential mapping opportunity between isoforms. The choice of quantification unit (event, intron cluster, LSV, transcript) determines which biological questions can be answered and which failure modes apply.
16
17	## Algorithmic Taxonomy
18
19	\| Family \| Unit \| Reference tools \| Fails when \|
20	\|--------\|------\|-----------------\|------------\|
21	\| Event-based \| Pre-defined SE/A5SS/A3SS/MXE/RI events from annotation \| rMATS-turbo, SUPPA2, VAST-TOOLS \| Event isn't in annotation; complex multi-junction events split arbitrarily; AFE/ALE confounded with splicing \|
22	\| LSV-based \| Local Splice Variations at single source/target nodes \| MAJIQ V3 \| Memory-constrained environments; cohorts smaller than ~3 reps; non-academic users (license) \|
23	\| Junction-cluster \| Annotation-free intron clusters by shared splice sites \| leafcutter, leafcutter2 \| Undersampled clusters lose power; topology biologically uninterpretable for novel events \|
24	\| Splice-graph \| Graph nodes (non-overlapping exonic regions) \| Whippet, Shiba \| Whippet maintenance status uncertain since ~2022; complex multi-exon graphs \|
25	\| Coverage-aware (IR) \| Intron body coverage + flanking junctions \| IRFinder-S, S-IRFindeR, iREAD \| Confounded by overlapping exons, repeats, low mappability regions \|
26	\| Isoform-based \| Transcript abundance via EM \| Salmon/kallisto + tximport \| Salmon EM uncertainty propagates; many similar isoforms (TTN, MAPT) become indistinguishable \|
27
28	The agent's first decision is which family the question requires, not which tool. Switching family is the response to a tool failing within a family — switching tool within a family rarely fixes systematic blind spots.
29
30	## Event Taxonomy (Beyond Standard SE/A5SS/A3SS/MXE/RI)
31
32	\| Class \| Code \| Biology \| Detection caveat \|
33	\|-------\|------\|---------\|-------------------\|
34	\| Skipped exon (cassette) \| SE \| Default cassette-exon AS \| Most common; well-handled by all tools \|
35	\| Alternative 5' splice site \| A5SS \| Alternative donor; intron 5' end varies \| Sign convention tool-specific (see below) \|
36	\| Alternative 3' splice site \| A3SS \| Alternative acceptor; intron 3' end varies \| Sensitive to BPS cancer mutations (SF3B1) — cryptic 3'ss ~10-30nt upstream \|
37	\| Mutually exclusive exons \| MXE \| Two exons paired, one included \| Tool implementations vary; verify which "form 1" is yours \|
38	\| Retained intron \| RI \| Whole intron retained in mature mRNA \| Junction-only quant systematically underdetects; needs IRFinder-S \|
39	\| Microexon \| (sub-SE) \| 3-27 nt; neural-enriched, SRRM4-regulated \| Missed by default aligner anchor lengths (>=20-30 nt); needs VAST-TOOLS, MicroExonator, or long-read \|
40	\| Exitron \| n/a \| Intronic region within an annotated CDS exon \| Mis-classified as A5SS/A3SS by most tools; use ExitronFinder, ScanExitron \|
41	\| Alternative first exon (AFE) \| AFE \| Alternative TSS / promoter use \| Promoter-driven, NOT spliceosomal; confirm with FANTOM CAGE before reporting as splicing \|
42	\| Alternative last exon (ALE) \| ALE \| Alternative cleavage/polyadenylation \| APA-driven, NOT spliceosomal; confirm with 3'-end-seq \|
43	\| Detained intron (DI) \| (RI subtype) \| Nuclear-retained on mature mRNA, regulated by Clk kinases \| Distinct from cytoplasmic NMD-targeted RI (Boutz 2015 Genes Dev); requires fractionation to confirm \|
44	\| Recursive splicing \| (intron subtype) \| Long introns >50kb spliced via inter

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splicing-quantification

1.1kstars185forks

View on GitHub

How to install splicing-quantification?

gptomics/bioskills/splicing-quantification

$npx -y skills add GPTomics/bioSkills --skill splicing-quantification

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	## Version Compatibility
2
3	Reference examples tested with: rMATS-turbo 4.3+, SUPPA2 2.4+, leafcutter 0.2.9+, MAJIQ 3.0+, IRFinder-S 2.0+, kallisto 0.50+, Salmon 1.10+, pandas 2.2+, STAR 2.7.11+
4
5	Before using code patterns, verify installed versions match. If versions differ:
6	- Python: `pip show <package>` then `help(module.function)` to check signatures
7	- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
8	- CLI: `<tool> --version` then `<tool> --help` to confirm flags
9
10	If code throws ImportError, AttributeError, or TypeError, introspect the installed
11	package and adapt the example to match the actual API rather than retrying.
12
13	# Splicing Quantification
14
15	Quantify alternative splicing events as PSI (percent spliced in) from RNA-seq. PSI = inclusion read evidence / (inclusion + skipping read evidence), normalized for differential mapping opportunity between isoforms. The choice of quantification unit (event, intron cluster, LSV, transcript) determines which biological questions can be answered and which failure modes apply.
16
17	## Algorithmic Taxonomy
18
19	\| Family \| Unit \| Reference tools \| Fails when \|
20	\|--------\|------\|-----------------\|------------\|
21	\| Event-based \| Pre-defined SE/A5SS/A3SS/MXE/RI events from annotation \| rMATS-turbo, SUPPA2, VAST-TOOLS \| Event isn't in annotation; complex multi-junction events split arbitrarily; AFE/ALE confounded with splicing \|
22	\| LSV-based \| Local Splice Variations at single source/target nodes \| MAJIQ V3 \| Memory-constrained environments; cohorts smaller than ~3 reps; non-academic users (license) \|
23	\| Junction-cluster \| Annotation-free intron clusters by shared splice sites \| leafcutter, leafcutter2 \| Undersampled clusters lose power; topology biologically uninterpretable for novel events \|
24	\| Splice-graph \| Graph nodes (non-overlapping exonic regions) \| Whippet, Shiba \| Whippet maintenance status uncertain since ~2022; complex multi-exon graphs \|
25	\| Coverage-aware (IR) \| Intron body coverage + flanking junctions \| IRFinder-S, S-IRFindeR, iREAD \| Confounded by overlapping exons, repeats, low mappability regions \|
26	\| Isoform-based \| Transcript abundance via EM \| Salmon/kallisto + tximport \| Salmon EM uncertainty propagates; many similar isoforms (TTN, MAPT) become indistinguishable \|
27
28	The agent's first decision is which family the question requires, not which tool. Switching family is the response to a tool failing within a family — switching tool within a family rarely fixes systematic blind spots.
29
30	## Event Taxonomy (Beyond Standard SE/A5SS/A3SS/MXE/RI)
31
32	\| Class \| Code \| Biology \| Detection caveat \|
33	\|-------\|------\|---------\|-------------------\|
34	\| Skipped exon (cassette) \| SE \| Default cassette-exon AS \| Most common; well-handled by all tools \|
35	\| Alternative 5' splice site \| A5SS \| Alternative donor; intron 5' end varies \| Sign convention tool-specific (see below) \|
36	\| Alternative 3' splice site \| A3SS \| Alternative acceptor; intron 3' end varies \| Sensitive to BPS cancer mutations (SF3B1) — cryptic 3'ss ~10-30nt upstream \|
37	\| Mutually exclusive exons \| MXE \| Two exons paired, one included \| Tool implementations vary; verify which "form 1" is yours \|
38	\| Retained intron \| RI \| Whole intron retained in mature mRNA \| Junction-only quant systematically underdetects; needs IRFinder-S \|
39	\| Microexon \| (sub-SE) \| 3-27 nt; neural-enriched, SRRM4-regulated \| Missed by default aligner anchor lengths (>=20-30 nt); needs VAST-TOOLS, MicroExonator, or long-read \|
40	\| Exitron \| n/a \| Intronic region within an annotated CDS exon \| Mis-classified as A5SS/A3SS by most tools; use ExitronFinder, ScanExitron \|
41	\| Alternative first exon (AFE) \| AFE \| Alternative TSS / promoter use \| Promoter-driven, NOT spliceosomal; confirm with FANTOM CAGE before reporting as splicing \|
42	\| Alternative last exon (ALE) \| ALE \| Alternative cleavage/polyadenylation \| APA-driven, NOT spliceosomal; confirm with 3'-end-seq \|
43	\| Detained intron (DI) \| (RI subtype) \| Nuclear-retained on mature mRNA, regulated by Clk kinases \| Distinct from cytoplasmic NMD-targeted RI (Boutz 2015 Genes Dev); requires fractionation to confirm \|
44	\| Recursive splicing \| (intron subtype) \| Long introns >50kb spliced via inter

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