cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.dj5pmm
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Acrocephalus vaughani (Sharpe, 1900)"
 ]
}

 The dataset includes 32 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059540-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bn3d2e
title: Occurrence Download

description: A dataset containing 13964 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Puma concolor (Linnaeus, 1771)"
 ]
}

 The dataset includes 13964 records from 258 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001450-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e8tkxb
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Stevia pohliana Baker",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037401-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3fdrur
title: Occurrence Download

description: A dataset containing 4129 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Loxigilla barbadensis Cory, 1886"
 ]
}

 The dataset includes 4129 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059507-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uzeyxh
title: Occurrence Download

description: A dataset containing 705 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ipomoea rubens Choisy)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 705 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045512-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y23ke8
title: Occurrence Download

description: A dataset containing 114552 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((91.37109 -13.10303,154.61719 -13.37681,156.6211 9.24091,87.99609 8.9632,91.37109 -13.10303))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Fabaceae"
 ]
}

 The dataset includes 114552 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0115388-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yfmxrk
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 {
 "or" : [
 "Country is Bulgaria",
 "Country is Albania",
 "Country is Croatia",
 "Country is Greece"
 ]
 },
 "Geometry POLYGON((7.89802 34.45610,38.10198 34.45610,38.10198 46.54390,7.89802 46.54390,7.89802 34.45610))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Linum elegans Boiss."
 ]
}

 The dataset includes 81 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0270108-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9x74p5
title: Occurrence Download

description: A dataset containing 4412 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melinna cristata (M.Sars, 1851)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is MANAGED"
 ]
 }
 },
 {
 "not" : {
 "EstablishmentMeans" : [
 "is not null"
 ]
 }
 }
 ]
 },
 {
 "or" : [
 "OccurrenceStatus is Present",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is not null"
 ]
 }
 }
 ]
 }
 ]
}

 The dataset includes 4412 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059538-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j5cmft
title: Occurrence Download

description: A dataset containing 1532 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Spodoptera frugiperda J.E.Smith, 1797"
 ]
}

 The dataset includes 1532 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198221-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9lscgt
title: Occurrence Download

description: A dataset containing 351 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Issue is Geodetic datum assumed WGS84",
 "Issue is Recorded date mismatch",
 "Issue is Recorded date invalid",
 "Issue is Recorded date unlikely"
 ]
 },
 "Year 1980-2018",
 "HasCoordinate is true",
 "TaxonKey is Brahea dulcis (Kunth) Mart.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 351 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037403-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zwq8bf
title: Occurrence Download

description: A dataset containing 306 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Malimbus cassini (Elliot, 1859)"
 ]
}

 The dataset includes 306 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059549-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nddzw6
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nychiodes ragusaria Millière, 1884"
 ]
}

 The dataset includes 18 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0199721-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yhnuae
title: Occurrence Download

description: A dataset containing 1179 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Abies religiosa (Kunth) Schltdl. & Cham."
 ]
}

 The dataset includes 1179 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037404-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cm8gp4
title: Occurrence Download

description: A dataset containing 2562074 species occurrences available in GBIF matching the query:
(Query is too complex. Can be viewed on the landing page)

 The dataset includes 2562074 records from 3127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012809-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y7dxjt
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anthurium gymnopus Griseb."
 ]
}

 The dataset includes 47 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0270751-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cxymml
title: Occurrence Download

description: A dataset containing 13841 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Elasmobranchii",
 "HasCoordinate is TRUE",
 "Country is United Kingdom of Great Britain and Northern Ireland"
 ]
}

 The dataset includes 13841 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014656-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6her34
title: Occurrence Download

description: A dataset containing 103242 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Canis lupus Linnaeus, 1758"
 ]
}

 The dataset includes 103242 records from 491 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0257819-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7sueuk
title: Occurrence Download

description: A dataset containing 368 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Glaucidium brasilianum cactorum van Rossem, 1937"
 ]
}

 The dataset includes 368 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033697-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j9mj9f
title: Occurrence Download

description: A dataset containing 107997 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1900-2018",
 "HasCoordinate is true",
 "TaxonKey is Veronica persica Poir.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 107997 records from 489 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014656-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tta93b
title: Occurrence Download

description: A dataset listing the 17 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Reef Check in Taiwan 台灣珊瑚礁體檢"
 ]
}

 The dataset's 17 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0256813-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tytgbm
title: Occurrence Download

description: A dataset containing 903 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((9.13611 0.16548,125.86389 0.16548,125.86389 46.83452,9.13611 46.83452,9.13611 0.16548))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Felis chaus Schreber, 1777"
 ]
}

 The dataset includes 903 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0257817-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gstnpq
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Chamaedorea metallica O.F.Cook ex H.E.Moore"
 ]
}

 The dataset includes 80 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059762-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e56vsj
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-103.14043 16.12994,31.14043 16.12994,31.14043 69.87006,-103.14043 69.87006,-103.14043 16.12994))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Neocyttus helgae (Holt & Byrne, 1908)"
 ]
}

 The dataset includes 20 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011387-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h62dyx
title: Occurrence Download

description: A dataset containing 137823 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ludwigia L."
 ]
}

 The dataset includes 137823 records from 898 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0235993-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mf98sx
title: Occurrence Download

description: A dataset containing 3701 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Pecari tajacu (Linnaeus, 1758)"
 ]
}

 The dataset includes 3701 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013677-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nfkadh
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Streptomyces minutiscleroticus (Thirumalachar, 1965) Pridham, 1970"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013678-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wbznwk
title: Occurrence Download

description: A dataset containing 111258 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "DatasetKey is EOD – eBird Observation Dataset",
 "OccurrenceStatus is Present",
 "TaxonKey is Vermivora chrysoptera (Linnaeus, 1766)",
 "Year 2014-2025"
 ]
}

 The dataset includes 111258 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003835-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10467234
title: Processed cell cycle-dependent gene expression (scRNA-seq) mESC data

description: Processed scRNA-seq data for the paper "Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data". 

This a reprocessed scRNA-seq dataset of mouse embryonic stem cells (mESCs) with inhibited differentiation, originally generated by Riba et al. (2019) using the 10x Genomics Chromium platform, containing spliced and unspliced transcript counts for over 5000 cells and more than 10000 genes. We have reprocessed the original FASTQ data deposited by the authors in the GEO database and reapplied DeepCycle (from Riba et al. (2019)) to extract the transcriptional phase information and associate each cell with a specific cell-cycle phase (G1, S and G2/M). See the manuscript for more details. 

The uploaded .h5ad file is an AnnData object, which contains the spliced and unspliced discrete mRNA transcript count (UMI) matrices for all cells and genes in the mESC population, as well as the cell-specific transcriptional phase and cell-cycle phase information. The dataset is used for the mechanistic model-based inference and analysis presented in the paper.
DOI: 10.15468/dl.tbw322
title: Occurrence Download

description: A dataset containing 1374 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 GBIF_ISEA3HCODE(16, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)) isea3hcellcode,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 (occurrence.level0gid = 'UKR' OR occurrence.level1gid = 'UKR' OR occurrence.level2gid = 'UKR' OR occurrence.level3gid = 'UKR')
 AND occurrence.hascoordinate = TRUE
 AND occurrence.hasgeospatialissues = FALSE
 AND occurrence.isincluster = FALSE
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.taxonkey = 5389029 OR occurrence.acceptedtaxonkey = 5389029 OR occurrence.kingdomkey = 5389029 OR occurrence.phylumkey = 5389029 OR occurrence.classkey = 5389029 OR occurrence.orderkey = 5389029 OR occurrence.familykey = 5389029 OR occurrence.genuskey = 5389029 OR occurrence.specieskey = 5389029)
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL AND occurrence.hascoordinate = TRUE)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year",
 GBIF_ISEA3HCODE(16, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000))

 The dataset's 1374 records were derived from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003839-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15032401
title: SpliceHarmonization: a harmonized method for identifying RNA splicing events in therapeutics for splicing modulation

description: GitHub link: https://github.com/interactivereport/SpliceHarmonization

Data Release:



simulation_data: Demonstrates the processed splicing event simulation.


simulation_data├── bam (# all simulated bam files for splicing analysis)├── fasta│   ├── combined_alt.fasta│   ├── combined_ref.fasta│   └── true_event_df.csv (# true simulated splicing event)├── simulation_num_{counts}_{alternative2control ratio}



SMN2_public_dataset: Contains all splicing analyses for one SMN2 public dataset (SRP334251), including rMATS, LeafCutter, MAJIQ, and SpliceHarmonization.


SMN2_public_dataset├── Original_res│   ├── bam  # (bam files removed due to size limitation, happy to disuccss!)│   ├── leafcutter│   ├── majiq│   ├── rmats│   └── stringtie└── SpliceHarmonization_res    └── {Comparison}        ├── harm        ├── harm_run_1.e.log        ├── harm_run_1.o.log        ├── harm_run_2.e.log        ├── harm_run_2.o.log        ├── harm_run_3.e.log        ├── harm_run_3.o.log        ├── harm_run_4.e.log        ├── harm_run_4.o.log        ├── junction_prep        ├── out        │   ├── all_cleaned.csv        │   ├── all_gene        │   │   ├── {gene_names}.csv (# events output for each gene)        │   └── mxe        ├── run1.sh        ├── run2.sh        ├── run3.sh        └── run4.sh



simulation_validation: Contains all splicing analyses for a simulation dataset, including rMATS, LeafCutter, MAJIQ, and SpliceHarmonization.


simulation_validation├── Original_res│   ├── leafcutter│   ├── majiq│   ├── rmats│   └── stringtie└── SpliceHarmonization_res    ├── {Comparison}    │   ├── harm    │   ├── harm_run_1.e.log    │   ├── harm_run_1.o.log    │   ├── harm_run_2.e.log    │   ├── harm_run_2.o.log    │   ├── harm_run_3.e.log    │   ├── harm_run_3.o.log    │   ├── harm_run_4.e.log    │   ├── harm_run_4.o.log    │   ├── junction_prep    │   ├── out    │   │   ├── all_cleaned.csv    │   │   ├── all_gene    │   │   │   ├── {gene_names}.csv (# events output for each gene)    │   │   ├── introns.csv    │   │   └── mxe    └── FinalMetric.csv (# summary evaluation information)

 

Files/folders in bold are final outputs
DOI: 10.5281/zenodo.15032402
title: SpliceHarmonization: a harmonized method for identifying RNA splicing events in therapeutics for splicing modulation

description: GitHub link: https://github.com/interactivereport/SpliceHarmonization

Data Release:



simulation_data: Demonstrates the processed splicing event simulation.


simulation_data├── bam (# all simulated bam files for splicing analysis)├── fasta│   ├── combined_alt.fasta│   ├── combined_ref.fasta│   └── true_event_df.csv (# true simulated splicing event)├── simulation_num_{counts}_{alternative2control ratio}



SMN2_public_dataset: Contains all splicing analyses for one SMN2 public dataset (SRP334251), including rMATS, LeafCutter, MAJIQ, and SpliceHarmonization.


SMN2_public_dataset├── Original_res│   ├── bam  # (bam files removed due to size limitation, happy to disuccss!)│   ├── leafcutter│   ├── majiq│   ├── rmats│   └── stringtie└── SpliceHarmonization_res    └── {Comparison}        ├── harm        ├── harm_run_1.e.log        ├── harm_run_1.o.log        ├── harm_run_2.e.log        ├── harm_run_2.o.log        ├── harm_run_3.e.log        ├── harm_run_3.o.log        ├── harm_run_4.e.log        ├── harm_run_4.o.log        ├── junction_prep        ├── out        │   ├── all_cleaned.csv        │   ├── all_gene        │   │   ├── {gene_names}.csv (# events output for each gene)        │   └── mxe        ├── run1.sh        ├── run2.sh        ├── run3.sh        └── run4.sh



simulation_validation: Contains all splicing analyses for a simulation dataset, including rMATS, LeafCutter, MAJIQ, and SpliceHarmonization.


simulation_validation├── Original_res│   ├── leafcutter│   ├── majiq│   ├── rmats│   └── stringtie└── SpliceHarmonization_res    ├── {Comparison}    │   ├── harm    │   ├── harm_run_1.e.log    │   ├── harm_run_1.o.log    │   ├── harm_run_2.e.log    │   ├── harm_run_2.o.log    │   ├── harm_run_3.e.log    │   ├── harm_run_3.o.log    │   ├── harm_run_4.e.log    │   ├── harm_run_4.o.log    │   ├── junction_prep    │   ├── out    │   │   ├── all_cleaned.csv    │   │   ├── all_gene    │   │   │   ├── {gene_names}.csv (# events output for each gene)    │   │   ├── introns.csv    │   │   └── mxe    └── FinalMetric.csv (# summary evaluation information)

 

Files/folders in bold are final outputs