Mercurial > repos > goeckslab > bayestme_deconvolve
changeset 0:4f6d716e5da2 draft
planemo upload for repository https://github.com/goeckslab/tools-st/tree/main/tools/bayesTME commit 26edd05a863adac97cb54a9fb2ae5613ce95df50
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deconvolve.xml Wed Dec 03 19:49:22 2025 +0000 @@ -0,0 +1,242 @@ +<tool id="bayestme_deconvolve" name="BayesTME: Deconvolve" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Reference-free and Reference-based Spot Deconvolution for Spatial Transcriptomics with BayesTME</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bayestme_requirements"/> + <command detect_errors="aggressive"><![CDATA[ + + ## Filtering Step (optional) + #if str($filter_genes.pre_filter) == 'filter_genes': + + filter_genes + --adata '${adata}' + --output 'dataset_filtered.h5ad' + --n-top-by-standard-deviation '${n_top_by_standard_deviation}' + #if str($spot_threshold) + --spot-threshold '${spot_threshold}' + #end if + #if $filter_ribosomal_genes + --filter-ribosomal-genes + #end if + #if $mode.deconv_mode == 'reference_based' + --expression-truth '${mode.expression_truth}' + #end if + #if $verbose + -v + #end if + && + #else + + ## Just use unfiltered + ln -s '${adata}' 'dataset_filtered.h5ad' && + + #end if + + ## Deconvolve Step + deconvolve + --adata 'dataset_filtered.h5ad' + --adata-output 'dataset_deconvolved.h5ad' + --output 'deconvolution_samples.h5' + #if $mode.deconv_mode == 'reference_free' + --n-components '${mode.n_components}' + #end if + #if $mode.deconv_mode == 'reference_based' + --expression-truth '${mode.expression_truth}' + --reference-scrna-celltype-column '${mode.reference_scrna_celltype_column}' + --reference-scrna-sample-column '${mode.reference_scrna_sample_column}' + #end if + --spatial-smoothing-parameter '${deconv_params.spatial_smoothing_parameter}' + --n-samples '${deconv_params.n_samples}' + --n-svi-steps '${deconv_params.n_svi_steps}' + #if $deconv_params.use_spatial_guide + --use-spatial-guide + #else + --no-use-spatial-guide + #end if + #if $additional_cli.verbose + -v + #end if + #if str($additional_cli.seed) + --seed '${additional_cli.seed}' + #end if + + ]]></command> + + <inputs> + + <!-- Required Input ST Data --> + <param argument="--adata" type="data" format="h5ad" label="Input AnnData in h5 format, expected to be already bleed corrected"/> + + <!-- Filter Genes Options (from macros) --> + <conditional name="filter_genes"> + <param name="pre_filter" type="select" label="Optional: Filter Genes By Spatial Variance Prior To Deconvolution" > + <option value="no_filtering" selected="true">No Filtering</option> + <option value="filter_genes">Filter Genes Prior To Deconvolution</option> + </param> + <when value="no_filtering"> + </when> + <when value="filter_genes"> + <expand macro="filter_genes_options" /> + </when> + </conditional> + + <!-- Deconvolution Strategy --> + <conditional name="mode"> + + <param name="deconv_mode" type="select" label="Deconvolution Strategy"> + <option value="reference_free" selected="true">Reference-free (unsupervised)</option> + <option value="reference_based">Reference-based (with scRNA reference)</option> + </param> + + <!-- Reference-free: Specify Number of Cell Types --> + <when value="reference_free"> + <param argument="--n-components" type="integer" optional="false" label="Number of cell types to deconvolve into"/> + </when> + + <!-- Reference-based: Provide scRNA Ref --> + <when value="reference_based"> + <param argument="--expression-truth" type="data" format="h5ad" optional="true" label="Matched scRNA data in h5ad format, will be used to enforce a prior on celltypes and expression"/> + <param argument="--reference-scrna-celltype-column" type="text" label="The name of the column with celltype id in the matched scRNA anndata"/> + <param argument="--reference-scrna-sample-column" type="text" label="The name of the column with sample id in the matched scRNA anndata"/> + </when> + + </conditional> + + <!-- Deconvolution Parameters --> + <section name="deconv_params" title="Deconvolution Parameters" expanded="false"> + <param argument="--spatial-smoothing-parameter" type="float" value="0.5" label="Spatial smoothing parameter (referred to as lambda in paper)"/> + <param argument="--n-samples" type="integer" value="100" label="Number of samples from the posterior distribution or variational family"/> + <param argument="--n-svi-steps" type="integer" value="20000" label="Number of steps for fitting variational family"/> + <param name="use_spatial_guide" argument="--use-spatial-guide, --no-use-spatial-guide" type="boolean" checked="true" label="Use spatial guide (variational family with spatial priors) for SVI"/> + </section> + + <!-- Additional CLI Options --> + <section name="additional_cli" title="Additional Arguments" expanded="false"> + <param argument="--seed" type="integer" optional="true" label="Seed value for random number generator"/> + <param argument="--verbose" type="boolean" checked="false" label="Enable verbose logging"/> + </section> + + </inputs> + + <outputs> + <data name="adata_output" format="h5ad" label="BayesTME Deconvolve on ${on_string}: dataset_deconvolved.h5ad" from_work_dir="dataset_deconvolved.h5ad"/> + <data name="output" format="h5" label="BayesTME Deconvolve on ${on_string}: deconvolution_samples.h5" from_work_dir="deconvolution_samples.h5"/> + <data name="deconvolution_loss" format="pdf" label="BayesTME Deconvolve on ${on_string}: deconvolution_loss.pdf" from_work_dir="deconvolution_loss.pdf"/> + </outputs> + + <tests> + + <!-- Reference-free Deconvolution Test --> + <test> + <param name="adata" value="visium_test_dataset.h5ad"/> + <conditional name="mode" > + <param name="deconv_mode" value="reference_free"/> + <param name="n_components" value="3"/> + </conditional> + <section name="deconv_params" > + <param name="spatial_smoothing_parameter" value="0.5"/> + <param name="n_samples" value="10"/> + <param name="n_svi_steps" value="10"/> + </section> + <section name="additional_cli" > + <param name="seed" value="93"/> + </section> + <conditional name="filter_genes" > + <param name="pre_filter" value="filter_genes"/> + <param name="n_top_by_standard_deviation" value="40"/> + <section name="additional_filtering_options" > + <param name="filter_ribosomal_genes" value="true"/> + </section> + </conditional> + <output name="adata_output" file="refFree_test_data/dataset_deconvolved.h5ad" compare="sim_size" delta="20000"> + <assert_contents> + <has_h5_keys keys="obsm/bayestme_cell_type_counts,obsm/bayestme_cell_type_probabilities,varm/bayestme_omega,varm/bayestme_omega_difference,varm/bayestme_relative_expression,varm/bayestme_relative_mean_expression,uns/bayestme_n_cell_types"/> + </assert_contents> + </output> + <output name="output" file="refFree_test_data/deconvolution_samples.h5" compare="sim_size" delta="500000"> + <assert_contents> + <has_h5_keys keys="beta_trace,cell_num_total_trace,cell_prob_trace,expression_trace,losses,reads_trace"/> + </assert_contents> + </output> + <output name="deconvolution_loss" file="refFree_test_data/deconvolution_loss.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + </test> + + <!-- Reference-based Deconvolution Test --> + <test> + <param name="adata" value="visium_test_dataset.h5ad"/> + <conditional name="mode" > + <param name="deconv_mode" value="reference_based"/> + <param name="expression_truth" value="refBased_test_data/scRef_test_dataset.h5ad"/> + <param name="reference_scrna_celltype_column" value="cell_type"/> + <param name="reference_scrna_sample_column" value="donor_id"/> + </conditional> + <section name="deconv_params" > + <param name="spatial_smoothing_parameter" value="0.5"/> + <param name="n_samples" value="10"/> + <param name="n_svi_steps" value="10"/> + </section> + <section name="additional_cli" > + <param name="seed" value="93"/> + </section> + <conditional name="filter_genes" > + <param name="pre_filter" value="filter_genes"/> + <param name="n_top_by_standard_deviation" value="40"/> + <section name="additional_filtering_options" > + <param name="filter_ribosomal_genes" value="true"/> + </section> + </conditional> + <output name="adata_output" file="refBased_test_data/dataset_deconvolved.h5ad" compare="sim_size" delta="20000"> + <assert_contents> + <has_h5_keys keys="obsm/bayestme_cell_type_counts,obsm/bayestme_cell_type_probabilities,varm/bayestme_omega,varm/bayestme_omega_difference,varm/bayestme_relative_expression,varm/bayestme_relative_mean_expression,uns/bayestme_n_cell_types"/> + </assert_contents> + </output> + <output name="output" file="refBased_test_data/deconvolution_samples.h5" compare="sim_size" delta="500000"> + <assert_contents> + <has_h5_keys keys="beta_trace,cell_num_total_trace,cell_prob_trace,expression_trace,losses,reads_trace"/> + </assert_contents> + </output> + <output name="deconvolution_loss" file="refBased_test_data/deconvolution_loss.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + </test> + + </tests> + <help> +<![CDATA[ + +usage: deconvolve [-h] [--adata ADATA] [--adata-output ADATA_OUTPUT] [-i] [--output OUTPUT] [--seed SEED] [--n-components N_COMPONENTS] + [--spatial-smoothing-parameter SPATIAL_SMOOTHING_PARAMETER] [--n-samples N_SAMPLES] [--expression-truth EXPRESSION_TRUTH] + [--reference-scrna-celltype-column REFERENCE_SCRNA_CELLTYPE_COLUMN] [--reference-scrna-sample-column REFERENCE_SCRNA_SAMPLE_COLUMN] + [--n-svi-steps N_SVI_STEPS] [--use-spatial-guide | --no-use-spatial-guide] [-v] + +Deconvolve data + +options: + -h, --help show this help message and exit + --adata ADATA Input AnnData in h5 format, expected to be already bleed corrected + --adata-output ADATA_OUTPUT + A new AnnData in h5 format created with the deconvolution summary results appended. + -i, --inplace If provided, append deconvolution summary results to the --adata archive in place + --output OUTPUT Path where DeconvolutionResult will be written h5 format + --seed SEED Seed value for random number generator. + --n-components N_COMPONENTS + Number of cell types to deconvolve into. + --spatial-smoothing-parameter SPATIAL_SMOOTHING_PARAMETER + Spatial smoothing parameter (referred to as lambda in paper) + --n-samples N_SAMPLES + Number of samples from the posterior distribution or variational family. + --expression-truth EXPRESSION_TRUTH + Matched scRNA data in h5ad format, will be used to enforce a prior on celltypes and expression. + --reference-scrna-celltype-column REFERENCE_SCRNA_CELLTYPE_COLUMN + The name of the column with celltype id in the matched scRNA anndata. + --reference-scrna-sample-column REFERENCE_SCRNA_SAMPLE_COLUMN + The name of the column with sample id in the matched scRNA anndata. + --n-svi-steps N_SVI_STEPS + Number of steps for fitting variational family + --use-spatial-guide, --no-use-spatial-guide + Use spatial guide (variational family with spatial priors) for SVI + -v, --verbose Enable verbose logging + +]]> + </help> + <expand macro="citations"/> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 03 19:49:22 2025 +0000 @@ -0,0 +1,30 @@ +<macros> + <token name="@TOOL_VERSION@">0.0.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> + + <xml name="bayestme_requirements"> + <requirements> + <container type="docker">jeffquinnmsk/bayestme:0a7cde6acac2ffc34e8ad00b7fab75f869d80de2</container> + </requirements> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1016/j.cels.2023.06.003</citation> + </citations> + </xml> + + <xml name="filter_genes_options" > + + <param argument="--n-top-by-standard-deviation" type="integer" optional="false" label="Use the top N genes with the highest spatial variance"/> + + <!-- Additional filtering options --> + <section name="additional_filtering_options" title="Additional Filtering Parameters" expanded="false"> + <param argument="--spot-threshold" optional="true" type="float" label="Filter genes appearing in greater than the provided threshold of tissue spots"/> + <param argument="--filter-ribosomal-genes" type="boolean" checked="false" label="Filter ribosomal genes (based on gene name regex)"/> + </section> + + </xml> + +</macros> \ No newline at end of file
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refBased_test_data/marker_genes.csv Wed Dec 03 19:49:22 2025 +0000 @@ -0,0 +1,241 @@ +gene_name,rank_in_cell_type,cell_type +BRI3,0,1 +SRSF3,1,1 +IFITM3,2,1 +LSM3,3,1 +MYL6,4,1 +AGR2,5,1 +CPNE3,6,1 +TOMM5,7,1 +SNRPG,8,1 +MORF4L2,9,1 +APOE,10,1 +TOMM7,11,1 +RAD21,12,1 +GFRA1,13,1 +WBP1,14,1 +CCT2,15,1 +NAA20,16,1 +NOP10,17,1 +DHX30,18,1 +HLA-DRA,19,1 +KRT10,20,1 +RARRES2,21,1 +SRSF5,22,1 +HMGA1,23,1 +MT2A,24,1 +POMP,25,1 +TKT,26,1 +TMED10,27,1 +TSTD1,28,1 +CNIH4,29,1 +PSMD2,30,1 +RABEP1,31,1 +APEX1,32,1 +TYROBP,33,1 +BANF1,34,1 +SNRPE,35,1 +ACADSB,36,1 +HSP90AB1,37,1 +PRDX3,38,1 +CSTB,39,1 +CNIH4,0,2 +ACADSB,1,2 +TKT,2,2 +HSP90AB1,3,2 +RAD21,4,2 +WBP1,5,2 +CCT2,6,2 +HMGA1,7,2 +BANF1,8,2 +HLA-DRA,9,2 +TSTD1,10,2 +PSMD2,11,2 +POMP,12,2 +BRI3,13,2 +MT2A,14,2 +MORF4L2,15,2 +TOMM7,16,2 +RARRES2,17,2 +SNRPG,18,2 +APEX1,19,2 +AGR2,20,2 +NAA20,21,2 +NOP10,22,2 +TMED10,23,2 +TOMM5,24,2 +KRT10,25,2 +DHX30,26,2 +TYROBP,27,2 +PRDX3,28,2 +SRSF3,29,2 +SNRPE,30,2 +IFITM3,31,2 +RABEP1,32,2 +GFRA1,33,2 +LSM3,34,2 +CPNE3,35,2 +APOE,36,2 +SRSF5,37,2 +MYL6,38,2 +CSTB,39,2 +MT2A,0,3 +WBP1,1,3 +CSTB,2,3 +SRSF5,3,3 +NOP10,4,3 +TMED10,5,3 +SRSF3,6,3 +DHX30,7,3 +MYL6,8,3 +TYROBP,9,3 +TSTD1,10,3 +APOE,11,3 +CCT2,12,3 +RAD21,13,3 +CPNE3,14,3 +NAA20,15,3 +LSM3,16,3 +ACADSB,17,3 +RARRES2,18,3 +RABEP1,19,3 +TOMM5,20,3 +SNRPE,21,3 +TKT,22,3 +IFITM3,23,3 +PRDX3,24,3 +HMGA1,25,3 +HLA-DRA,26,3 +POMP,27,3 +HSP90AB1,28,3 +KRT10,29,3 +TOMM7,30,3 +MORF4L2,31,3 +BANF1,32,3 +APEX1,33,3 +AGR2,34,3 +SNRPG,35,3 +GFRA1,36,3 +PSMD2,37,3 +CNIH4,38,3 +BRI3,39,3 +RABEP1,0,4 +PRDX3,1,4 +HSP90AB1,2,4 +SNRPE,3,4 +TYROBP,4,4 +SRSF5,5,4 +RAD21,6,4 +RARRES2,7,4 +POMP,8,4 +NAA20,9,4 +TKT,10,4 +MYL6,11,4 +CCT2,12,4 +GFRA1,13,4 +SRSF3,14,4 +ACADSB,15,4 +NOP10,16,4 +TOMM7,17,4 +BANF1,18,4 +HMGA1,19,4 +APEX1,20,4 +CSTB,21,4 +TMED10,22,4 +AGR2,23,4 +TSTD1,24,4 +HLA-DRA,25,4 +CNIH4,26,4 +TOMM5,27,4 +MORF4L2,28,4 +PSMD2,29,4 +KRT10,30,4 +IFITM3,31,4 +LSM3,32,4 +DHX30,33,4 +MT2A,34,4 +WBP1,35,4 +CPNE3,36,4 +SNRPG,37,4 +APOE,38,4 +BRI3,39,4 +APEX1,0,5 +CPNE3,1,5 +CNIH4,2,5 +CSTB,3,5 +BANF1,4,5 +HLA-DRA,5,5 +TOMM5,6,5 +MT2A,7,5 +MYL6,8,5 +KRT10,9,5 +SNRPE,10,5 +TMED10,11,5 +POMP,12,5 +AGR2,13,5 +MORF4L2,14,5 +LSM3,15,5 +PRDX3,16,5 +APOE,17,5 +HSP90AB1,18,5 +TYROBP,19,5 +HMGA1,20,5 +NOP10,21,5 +DHX30,22,5 +CCT2,23,5 +SRSF3,24,5 +SNRPG,25,5 +PSMD2,26,5 +TSTD1,27,5 +GFRA1,28,5 +RABEP1,29,5 +WBP1,30,5 +TOMM7,31,5 +IFITM3,32,5 +TKT,33,5 +NAA20,34,5 +ACADSB,35,5 +RAD21,36,5 +RARRES2,37,5 +BRI3,38,5 +SRSF5,39,5 +PSMD2,0,6 +GFRA1,1,6 +DHX30,2,6 +SNRPG,3,6 +KRT10,4,6 +IFITM3,5,6 +APOE,6,6 +SNRPE,7,6 +LSM3,8,6 +SRSF5,9,6 +AGR2,10,6 +ACADSB,11,6 +TKT,12,6 +RARRES2,13,6 +HLA-DRA,14,6 +HMGA1,15,6 +TYROBP,16,6 +PRDX3,17,6 +NAA20,18,6 +BRI3,19,6 +TOMM7,20,6 +TSTD1,21,6 +BANF1,22,6 +RABEP1,23,6 +POMP,24,6 +MORF4L2,25,6 +CPNE3,26,6 +APEX1,27,6 +TOMM5,28,6 +CSTB,29,6 +TMED10,30,6 +NOP10,31,6 +RAD21,32,6 +WBP1,33,6 +MYL6,34,6 +CCT2,35,6 +HSP90AB1,36,6 +SRSF3,37,6 +CNIH4,38,6 +MT2A,39,6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refBased_test_data/omega.csv Wed Dec 03 19:49:22 2025 +0000 @@ -0,0 +1,41 @@ +,0,1,2,3,4,5 +AGR2,0.3,0.2,0.0,0.1,0.2,0.2 +MORF4L2,0.3,0.2,0.1,0.1,0.2,0.1 +SNRPE,0.0,0.1,0.1,0.3,0.2,0.3 +HSP90AB1,0.0,0.4,0.1,0.3,0.2,0.0 +GFRA1,0.2,0.1,0.0,0.2,0.1,0.4 +ACADSB,0.0,0.4,0.2,0.2,0.0,0.2 +APOE,0.2,0.0,0.2,0.0,0.2,0.4 +MT2A,0.1,0.3,0.4,0.0,0.2,0.0 +IFITM3,0.3,0.1,0.1,0.1,0.0,0.4 +KRT10,0.1,0.1,0.1,0.1,0.2,0.4 +HLA-DRA,0.1,0.3,0.1,0.1,0.2,0.2 +TSTD1,0.1,0.3,0.2,0.1,0.1,0.2 +CCT2,0.2,0.3,0.2,0.2,0.1,0.0 +WBP1,0.2,0.3,0.4,0.0,0.1,0.0 +TOMM5,0.3,0.2,0.1,0.1,0.2,0.1 +RAD21,0.2,0.3,0.2,0.3,0.0,0.0 +CNIH4,0.1,0.4,0.0,0.1,0.4,0.0 +TMED10,0.1,0.2,0.3,0.1,0.2,0.1 +TOMM7,0.2,0.2,0.1,0.2,0.1,0.2 +PRDX3,0.0,0.1,0.1,0.4,0.2,0.2 +LSM3,0.3,0.0,0.2,0.0,0.2,0.3 +NOP10,0.1,0.2,0.3,0.2,0.1,0.1 +HMGA1,0.1,0.3,0.1,0.2,0.1,0.2 +TYROBP,0.0,0.1,0.2,0.3,0.2,0.2 +RARRES2,0.1,0.2,0.2,0.3,0.0,0.2 +CSTB,0.0,0.0,0.4,0.2,0.3,0.1 +CPNE3,0.3,0.0,0.2,0.0,0.4,0.1 +BRI3,0.5,0.3,0.0,0.0,0.0,0.2 +SNRPG,0.3,0.2,0.0,0.0,0.1,0.4 +MYL6,0.3,0.0,0.3,0.2,0.2,0.0 +SRSF5,0.1,0.0,0.3,0.3,0.0,0.3 +POMP,0.1,0.3,0.1,0.2,0.2,0.1 +APEX1,0.1,0.2,0.0,0.2,0.4,0.1 +BANF1,0.0,0.3,0.1,0.2,0.3,0.1 +DHX30,0.1,0.1,0.3,0.0,0.1,0.4 +RABEP1,0.1,0.1,0.2,0.4,0.1,0.1 +SRSF3,0.3,0.1,0.3,0.2,0.1,0.0 +PSMD2,0.1,0.3,0.0,0.1,0.1,0.4 +NAA20,0.2,0.2,0.2,0.2,0.0,0.2 +TKT,0.1,0.4,0.1,0.2,0.0,0.2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refBased_test_data/relative_expression.csv Wed Dec 03 19:49:22 2025 +0000 @@ -0,0 +1,41 @@ +,0,1,2,3,4,5 +AGR2,-0.08380652219057083,-0.24061469733715057,-0.2815214991569519,-0.22048918902873993,-0.25506848096847534,0.08380652219057083 +MORF4L2,-0.23045410215854645,0.23045410215854645,-0.4615306854248047,-0.4566039443016052,-0.29516807198524475,-0.316114217042923 +SNRPE,-0.3119671046733856,-0.4708918631076813,-0.20415183901786804,-0.018912073224782944,-0.18750175833702087,0.018912073224782944 +HSP90AB1,-0.43157273530960083,-0.2963055372238159,-0.4264748990535736,0.2963055372238159,-0.4036998450756073,-0.5289340615272522 +GFRA1,-0.2077164351940155,-0.5465796589851379,-0.51600581407547,-0.11956971883773804,-0.42499789595603943,0.11956971883773804 +ACADSB,-0.4230344593524933,0.004193827509880066,-0.24471037089824677,-0.15493634343147278,-0.5466628074645996,-0.004193827509880066 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refFree_test_data/marker_genes.csv Wed Dec 03 19:49:22 2025 +0000 @@ -0,0 +1,121 @@ +gene_name,rank_in_cell_type,cell_type +S100A13,0,1 +GFRA1,1,1 +AGR2,2,1 +MORF4L2,3,1 +FN1,4,1 +HSBP1,5,1 +ENO1,6,1 +TTLL12,7,1 +LAPTM4B,8,1 +BST2,9,1 +KRT8,10,1 +NACA,11,1 +APOD,12,1 +HLA-DRA,13,1 +ARF1,14,1 +ACADSB,15,1 +SPP1,16,1 +CXCL14,17,1 +SNRPE,18,1 +IFITM3,19,1 +KRT19,20,1 +ATP5F1B,21,1 +S100P,22,1 +CTTN,23,1 +HSP90AB1,24,1 +BTF3,25,1 +TPI1,26,1 +SLC9A3R1,27,1 +PBX1,28,1 +APOE,29,1 +IDH2,30,1 +IER3,31,1 +TUBA1B,32,1 +MAGED2,33,1 +MT2A,34,1 +COX17,35,1 +TOMM6,36,1 +KRT10,37,1 +AGR3,38,1 +SELENOM,39,1 +SELENOM,0,2 +BTF3,1,2 +MAGED2,2,2 +S100P,3,2 +IFITM3,4,2 +COX17,5,2 +KRT10,6,2 +SLC9A3R1,7,2 +TPI1,8,2 +IER3,9,2 +ARF1,10,2 +TOMM6,11,2 +IDH2,12,2 +TUBA1B,13,2 +KRT8,14,2 +HLA-DRA,15,2 +BST2,16,2 +CXCL14,17,2 +KRT19,18,2 +APOE,19,2 +ENO1,20,2 +SPP1,21,2 +MORF4L2,22,2 +PBX1,23,2 +AGR2,24,2 +APOD,25,2 +ATP5F1B,26,2 +ACADSB,27,2 +NACA,28,2 +SNRPE,29,2 +HSBP1,30,2 +FN1,31,2 +AGR3,32,2 +LAPTM4B,33,2 +S100A13,34,2 +HSP90AB1,35,2 +GFRA1,36,2 +CTTN,37,2 +MT2A,38,2 +TTLL12,39,2 +AGR3,0,3 +MT2A,1,3 +TTLL12,2,3 +HSP90AB1,3,3 +CTTN,4,3 +PBX1,5,3 +APOE,6,3 +ATP5F1B,7,3 +LAPTM4B,8,3 +TOMM6,9,3 +KRT10,10,3 +SNRPE,11,3 +ACADSB,12,3 +TUBA1B,13,3 +NACA,14,3 +APOD,15,3 +IDH2,16,3 +HSBP1,17,3 +FN1,18,3 +IER3,19,3 +GFRA1,20,3 +SELENOM,21,3 +SPP1,22,3 +KRT19,23,3 +COX17,24,3 +S100A13,25,3 +CXCL14,26,3 +HLA-DRA,27,3 +ENO1,28,3 +MAGED2,29,3 +AGR2,30,3 +MORF4L2,31,3 +BST2,32,3 +SLC9A3R1,33,3 +KRT8,34,3 +TPI1,35,3 +S100P,36,3 +ARF1,37,3 +BTF3,38,3 +IFITM3,39,3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refFree_test_data/omega.csv Wed Dec 03 19:49:22 2025 +0000 @@ -0,0 +1,41 @@ +,0,1,2 +CXCL14,0.4,0.4,0.2 +AGR2,0.5,0.3,0.2 +KRT8,0.4,0.4,0.2 +MORF4L2,0.5,0.3,0.2 +IER3,0.2,0.5,0.3 +FN1,0.5,0.2,0.3 +S100A13,0.5,0.2,0.3 +SNRPE,0.3,0.3,0.4 +HSBP1,0.5,0.2,0.3 +CTTN,0.3,0.2,0.5 +S100P,0.3,0.6,0.1 +TUBA1B,0.2,0.5,0.3 +PBX1,0.2,0.3,0.5 +ARF1,0.4,0.5,0.1 +HSP90AB1,0.3,0.2,0.5 +GFRA1,0.5,0.2,0.3 +SLC9A3R1,0.3,0.5,0.2 +ACADSB,0.4,0.3,0.3 +APOE,0.2,0.4,0.4 +MAGED2,0.2,0.6,0.2 +ATP5F1B,0.3,0.3,0.4 +TTLL12,0.4,0.0,0.6 +KRT19,0.3,0.4,0.3 +MT2A,0.2,0.2,0.6 +IFITM3,0.3,0.6,0.1 +BST2,0.4,0.4,0.2 +ENO1,0.4,0.4,0.2 +TPI1,0.3,0.5,0.2 +SPP1,0.4,0.3,0.3 +SELENOM,0.0,0.7,0.3 +AGR3,0.1,0.2,0.7 +LAPTM4B,0.4,0.2,0.4 +NACA,0.4,0.3,0.3 +IDH2,0.2,0.5,0.3 +BTF3,0.3,0.6,0.1 +TOMM6,0.1,0.5,0.4 +KRT10,0.1,0.5,0.4 +HLA-DRA,0.4,0.4,0.2 +COX17,0.2,0.5,0.3 +APOD,0.4,0.3,0.3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refFree_test_data/relative_expression.csv Wed Dec 03 19:49:22 2025 +0000 @@ -0,0 +1,41 @@ +,0,1,2 +CXCL14,-0.4375229477882385,-0.16171614825725555,0.16171614825725555 +AGR2,0.17474493384361267,-0.17474493384361267,-0.25233936309814453 +KRT8,-0.17429867386817932,0.17429867386817932,-0.5132394433021545 +MORF4L2,0.13628606498241425,-0.13628606498241425,-0.2668810486793518 +IER3,-0.37387657165527344,0.3328932821750641,-0.3328932821750641 +FN1,0.1353853940963745,-0.37078720331192017,-0.1353853940963745 +S100A13,0.46118298172950745,-0.46118298172950745,-0.5808185338973999 +SNRPE,0.4548073410987854,-0.6118611693382263,-0.4548073410987854 +HSBP1,0.0903487578034401,-0.23363488912582397,-0.0903487578034401 +CTTN,-0.2016545981168747,-0.6537009477615356,0.2016545981168747 +S100P,-0.17843392491340637,0.1432689130306244,-0.1432689130306244 +TUBA1B,-0.4132199287414551,-0.21157126128673553,0.21157126128673553 +PBX1,0.11901863664388657,-0.13771884143352509,-0.11901863664388657 +ARF1,-0.3169371485710144,0.3169371485710144,-0.422046959400177 +HSP90AB1,-0.26272037625312805,-0.4617912769317627,0.26272037625312805 +GFRA1,0.3331877291202545,-0.4742777347564697,-0.3331877291202545 +SLC9A3R1,-0.3606945276260376,0.3606945276260376,-0.40291425585746765 +ACADSB,-0.36930787563323975,-0.44669845700263977,0.36930787563323975 +APOE,-0.18534696102142334,-0.33504199981689453,0.18534696102142334 +MAGED2,-0.47810444235801697,0.2290552854537964,-0.2290552854537964 +ATP5F1B,-0.03063628077507019,-0.29607343673706055,0.03063628077507019 +TTLL12,0.14046917855739594,-0.708142876625061,-0.14046917855739594 +KRT19,0.18354931473731995,-0.18354931473731995,-0.47579142451286316 +MT2A,-0.5393160581588745,-0.6572124361991882,0.5393160581588745 +IFITM3,0.19224987924098969,-0.19224987924098969,-0.6451092958450317 +BST2,-0.1251307874917984,0.1251307874917984,-0.3095334470272064 +ENO1,0.17155671119689941,-0.40797799825668335,-0.17155671119689941 +TPI1,-0.34889811277389526,0.34889811277389526,-0.5328922867774963 +SPP1,-0.3826879858970642,0.3826879858970642,-0.42629218101501465 +SELENOM,-0.5283265709877014,0.34312599897384644,-0.34312599897384644 +AGR3,-0.7603973150253296,-0.4380464553833008,0.4380464553833008 +LAPTM4B,-0.024069825187325478,-0.4395749866962433,0.024069825187325478 +NACA,-0.18196161091327667,-0.5017327666282654,0.18196161091327667 +IDH2,-0.33073437213897705,-0.07798266410827637,0.07798266410827637 +BTF3,-0.28069669008255005,0.28069669008255005,-0.5261001586914062 +TOMM6,-0.36111515760421753,0.12757104635238647,-0.12757104635238647 +KRT10,-0.46817606687545776,0.39888796210289,-0.39888796210289 +HLA-DRA,-0.2194845974445343,0.15029479563236237,-0.15029479563236237 +COX17,-0.549075722694397,0.47629469633102417,-0.47629469633102417 +APOD,-0.19722692668437958,-0.17616669833660126,0.17616669833660126