Mercurial > repos > iuc > cosg
changeset 0:cf880680fd0b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
| author | iuc |
|---|---|
| date | Thu, 30 May 2024 11:10:21 +0000 |
| parents | |
| children | fe5996e87b41 |
| files | cosg.xml macros.xml test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_2.h5ad test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_3.h5ad test-data/marker_1.tsv test-data/marker_2.tsv test-data/marker_3.tsv test-data/tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced.h5ad |
| diffstat | 9 files changed, 317 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cosg.xml Thu May 30 11:10:21 2024 +0000 @@ -0,0 +1,202 @@ +<tool id="cosg" name="COSG" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@"> + <description>Cell marker gene identification</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + </expand> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ +@CMD@ + ]]></command> + <configfiles> + <configfile name="script_file"><![CDATA[ +@CMD_imports@ +@CMD_read_inputs@ + +#if $method_options.groups != 'all' + #set $method_options.groups=[$groups] +#end if + +cosg.cosg(adata, + groupby='$method_options.groupby', + groups='$method_options.groups', + n_genes_user=$method_options.n_genes_user, + mu=$advanced_options.mu, + remove_lowly_expressed=$advanced_options.filter_expression.remove_lowly_expressed, + #if $advanced_options.filter_expression.remove_lowly_expressed == "True" + expressed_pct=$advanced_options.filter_expression.expressed_pct, + #end ifs + key_added='$advanced_options.key_added', + use_raw=$advanced_options.layer_selection.use_raw, + #if $advanced_options.layer_selection.use_raw == "False" + #if $advanced_options.layer_selection.layer + layer='$advanced_options.layer_selection.layer', + #end if + #end if + reference='$advanced_options.reference' + ) + +df=pd.DataFrame(adata.uns['cosg']['names']).T +df.to_csv('marker.tsv', sep='\t', index=True) + +@CMD_anndata_write_outputs@ +]]></configfile> + </configfiles> + <inputs> + <expand macro="inputs_anndata"/> + <section name="method_options" title="Method Options" expanded="true"> + <param argument="groupby" type="text" value="" optional="false" label="The key of the cell groups in .obs"/> + <param argument="groups" type="text" value="all" optional="false" label="Subset of cell groups" help="e.g. 'g1','g2','g3'."/> + <param argument="n_genes_user" type="integer" value="50" min="1" label="The number of genes that appear in the returned tables"/> + </section> + <section name="advanced_options" title="Advanced Options"> + <param argument="mu" type="float" value="1.0" min="0.0" max="1.0" label="The penalty restricting marker genes expressing in non-target cell groups" help="Larger value represents more strict restrictions. mu should be >= 0, and by default, mu = 1."/> + <conditional name="filter_expression"> + <param name="remove_lowly_expressed" type="select" label="Remove lowly expressed genes" help="If yes, genes that express a percentage of target cells smaller than a specific value (`expressed_pct`) are not considered as marker genes for the target cells."> + <option value="False">No</option> + <option value="True">Yes</option> + </param> + <when value="False"/> + <when value="True"> + <param argument="expressed_pct" type="float" value="0.1" min="0.01" max="1.0" label="Percentage of target cells" help="Genes that express a percentage of target cells smaller than a specific value (`expressed_pct`) are not considered as marker genes for the target cells."/> + </when> + </conditional> + <param argument="key_added" type="text" value="cosg" optional="false" label="The key in adata.uns information is saved to."> + <validator type="empty_field"/> + </param> + <conditional name="layer_selection"> + <param name="use_raw" type="select" label="Use raw attribute of adata if present to perform tests on." help="If use_raw is set to True then adata.raw.X if it exists."> + <option value="False">No</option> + <option value="True">Yes</option> + </param> + <when value="False"> + <param argument="layer" type="text" value="" label="Key from adata.layers whose value will be used to perform tests on." help="If empty then adata.X will be used. If use_raw is set to True then adata.raw.X. If layers specified then use adata.layers[layer]."/> + </when> + <when value="True"/> + </conditional> + <param argument="reference" type="text" value="rest" optional="false" label="If a group identifier, compare with respect to this group." help=" If you use the keyword 'rest', compare each group to the union of the rest of the group."> + <validator type="empty_field"/> + </param> + </section> + <expand macro="inputs_common_advanced"/> + </inputs> + <outputs> + <expand macro="anndata_outputs"/> + <data name="marker_out" format="tabular" from_work_dir="marker.tsv" label="${tool.name} on ${on_string}: Markers"/> + </outputs> + <tests> + <test expect_num_outputs="3"> + <!-- test 1 --> + <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced.h5ad" /> + <param name="groupby" value="bulk_labels"/> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="cosg.cosg"/> + <has_text_matching expression="groupby='bulk_labels'"/> + <has_text_matching expression="groups='all'"/> + <has_text_matching expression="n_genes_user=50"/> + <has_text_matching expression="mu=1.0"/> + <has_text_matching expression="remove_lowly_expressed=False"/> + <has_text_matching expression="key_added='cosg'"/> + <has_text_matching expression="use_raw=False"/> + <has_text_matching expression="reference='rest'"/> + </assert_contents> + </output> + <output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs, var, uns" /> + </assert_contents> + </output> + <output name="marker_out" file="marker_1.tsv" ftype="tabular" compare="sim_size"> + <assert_contents> + <has_n_columns n="51" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <!-- test 2 --> + <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced.h5ad" /> + <param name="groupby" value="louvain"/> + <param name="remove_lowly_expressed" value="True" /> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="cosg.cosg"/> + <has_text_matching expression="groupby='louvain'"/> + <has_text_matching expression="groups='all'"/> + <has_text_matching expression="n_genes_user=50"/> + <has_text_matching expression="mu=1.0"/> + <has_text_matching expression="remove_lowly_expressed=True"/> + <has_text_matching expression="expressed_pct=0.1"/> + <has_text_matching expression="key_added='cosg'"/> + <has_text_matching expression="use_raw=False"/> + <has_text_matching expression="reference='rest'"/> + </assert_contents> + </output> + <output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_2.h5ad" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs, var, uns" /> + </assert_contents> + </output> + <output name="marker_out" file="marker_2.tsv" ftype="tabular"> + <assert_contents> + <has_n_columns n="51" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <!-- test 3 --> + <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced.h5ad" /> + <param name="groupby" value="bulk_labels"/> + <param name="use_raw" value="True"/> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="cosg.cosg"/> + <has_text_matching expression="groupby='bulk_labels'"/> + <has_text_matching expression="groups='all'"/> + <has_text_matching expression="n_genes_user=50"/> + <has_text_matching expression="mu=1.0"/> + <has_text_matching expression="remove_lowly_expressed=False"/> + <has_text_matching expression="key_added='cosg'"/> + <has_text_matching expression="use_raw=True"/> + <has_text_matching expression="reference='rest'"/> + </assert_contents> + </output> + <output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_3.h5ad" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="obs, var, uns" /> + </assert_contents> + </output> + <output name="marker_out" file="marker_3.tsv" ftype="tabular"> + <assert_contents> + <has_n_columns n="51" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +Marker gene identification for single-cell sequencing data using COSG. +============================================================================================================ + +Accurate and fast cell marker gene identification with COSG + +COSG is a cosine similarity-based method for more accurate and scalable marker gene identification. + +- COSG is a general method for cell marker gene identification across different data modalities, e.g., scRNA-seq, scATAC-seq and spatially resolved transcriptome data. +- Marker genes or genomic regions identified by COSG are more indicative and with greater cell-type specificity. +- COSG is ultrafast for large-scale datasets, and is capable of identifying marker genes for one million cells in less than two minutes. + +Here is the R version for COSG, and the Python version is hosted in https://github.com/genecell/COSG. + + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu May 30 11:10:21 2024 +0000 @@ -0,0 +1,85 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@profile@">22.05</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">cosg</requirement> + <requirement type="package" version="1.9.8">scanpy</requirement> + <requirement type="package" version="1.5.3">pandas</requirement> + <requirement type="package" version="3.7">matplotlib</requirement> + <requirement type="package" version="0.12.2">seaborn</requirement> + <yield /> + </requirements> + </xml> + <xml name="creators"> + <creator> + <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" /> + </creator> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bib/bbab579</citation> + <citation type="doi">10.1093/gigascience/giaa102</citation> + </citations> + </xml> + <xml name="version_command"> + <version_command><![CDATA[python -c "import cosg;import importlib.metadata;print('%s' % importlib.metadata.version('cosg'))"]]></version_command> + </xml> + <token name="@CMD@"><![CDATA[ +cp '$adata' 'anndata.h5ad' && +cat '$script_file' > '$hidden_output' && +python '$script_file' >> '$hidden_output' && +ls . >> '$hidden_output' && +touch 'anndata_info.txt' && +cat 'anndata_info.txt' @CMD_prettify_stdout@ + ]]> + </token> + <token name="@CMD_imports@"><![CDATA[ +import scanpy as sc +import pandas as pd +import numpy as np +import cosg + ]]> + </token> + <xml name="sanitize_query" token_validinitial="string.printable"> + <sanitizer> + <valid initial="@VALIDINITIAL@"> + <remove value="'" /> + </valid> + </sanitizer> + </xml> + <xml name="sanitize_vectors" token_validinitial="string.digits"> + <sanitizer> + <valid initial="@VALIDINITIAL@"> + <add value=","/> + </valid> + </sanitizer> + </xml> + <xml name="inputs_anndata"> + <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/> + </xml> + <token name="@CMD_read_inputs@"><![CDATA[ +adata = sc.read_h5ad('anndata.h5ad') +]]> + </token> + <xml name="inputs_common_advanced"> + <section name="advanced_common" title="Advanced Output Options" expanded="false"> + <param name="show_log" type="boolean" checked="false" label="Output Log?" /> + </section> + </xml> + <xml name="anndata_outputs"> + <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix"/> + <data name="hidden_output" format="txt" label="Log file" > + <filter>advanced_common['show_log']</filter> + </data> + </xml> + <token name="@CMD_anndata_write_outputs@"><![CDATA[ +adata.write_h5ad('anndata.h5ad') +with open('anndata_info.txt','w', encoding='utf-8') as ainfo: + print(adata, file=ainfo) +]]> + </token> + <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g" | sed -r 's|^\s*(.*):\s(.*)|[\1]\n- \2|g' | sed 's|, |\n- |g' + ]]></token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/marker_1.tsv Thu May 30 11:10:21 2024 +0000 @@ -0,0 +1,11 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 +CD14+ Monocyte PILRA PSAP CD68 TMEM176B FTL NPC2 LST1 FCGR3A FCER1G CEBPB FCN1 SERPINA1 OAZ1 CFD FTH1 HCK AIF1 SAT1 CTSS S100A11 MS4A7 TYROBP COTL1 STXBP2 RP11-290F20.3 S100A4 IFITM2 SPI1 DUSP1 SESN2 IFITM3 MPP1 GALE CORO1B RP11-390E23.6 VIMP RSBN1L-AS1 CHD4 CFP GSTP1 PFN1 FCGRT ADTRP ARHGDIB AMICA1 HLA-DRB5 CST3 GRN HLA-DPA1 SSR3 +CD19+ B TNFRSF13B CD79B SMARCB1 PNOC CCDC50 AL928768.3 BANK1 MS4A1 CD79A ISG20 IGLL5 TNFRSF17 KIAA0125 TPD52 PEBP1 FKBP11 CCDC132 SUB1 POU2AF1 MZB1 PTPRCAP UBE2J1 BLK SPIB DERL3 FAM63B MPHOSPH9 IGJ FCRLA XBP1 NCF1 SSR3 CD52 TSHZ2 PDLIM1 VIMP SSR4 S1PR4 SELL HMGA1 NUCB2 JUN CD27 ARHGDIB GYPC CALR ADTRP BTG1 EXOG RARRES3 +CD34+ PRSS57 C19orf77 SPINK2 RP11-620J15.3 SNHG7 CYTL1 EGFL7 NGFRAP1 SOX4 NFE2 EGR1 RP3-467N11.1 H1FX CDK6 SERPINB1 SPINT2 HMGA1 IL1B NUCB2 RPLP0 IGFBP7 RPLP1 ATXN7L3B RPS3 C1orf228 KIAA0125 RPL3 SYPL1 CD63 LDHB SEPT1 JUN FAM101B PRKCQ-AS1 MATK PEBP1 SELL ITM2A SSR3 SPON2 XBP1 UBE2J1 VIMP GYPC STK17A STMN1 VIM MZB1 HOPX CD99 +CD4+/CD25 T Reg IL32 SPOCK2 ACTG1 CD2 CD3D GPR171 ARHGDIB ACOX1 MAL SIT1 GIMAP4 AES CD52 SEPT1 TMSB10 LAT STMN1 LINC00402 CD27 TSHZ2 S1PR4 CD3E PFN1 CD99 AQP3 PTPRCAP CD3G LY9 LCK CD247 S100A4 CCR7 TTC39C CORO1B MPHOSPH9 FYB RPSA FLT3LG B2M GIMAP7 PRKCQ-AS1 SELL BTG1 CCDC132 GYPC DENND2D LDHB IL7R ITM2A RPLP0 +CD4+/CD45RA+/CD25- Naive T EAF2 GNG7 SSR4 CALR DERL3 MANF IGJ XBP1 ATXN7L3B SSR3 UBE2J1 CD79A MZB1 RP3-467N11.1 TNFRSF17 NCF1 CDK6 SUB1 POU2AF1 AL928768.3 FKBP11 VIMP GYPC JUN CD27 PEBP1 SMARCB1 FLT3LG RPLP1 RPLP0 CCDC50 ISG20 IGLL5 HCST GSTP1 GPX1 CD52 VIM PTPRCAP FCGRT CD74 B2M RPL3 CYTL1 SPINK2 PRSS57 C19orf77 RP11-620J15.3 FAM101B CCDC132 +CD4+/CD45RO+ Memory RNF138 NOSIP IFITM1 LCK RARRES3 ALOX5AP FAM63B RAB3IP GZMK CD3G SEPT1 LDHB SELL CD3D EXOG RPSA CD247 AES CD52 TMSB10 NUCB2 DENND2D RPL3 RPLP1 ACTG1 FYB GIMAP7 CORO1B LY9 CD7 PFN1 RPS3 GYPC CD2 ARHGDIB IL32 RPLP0 CD99 CD3E GIMAP4 HCST B2M LAT ISG20 ITM2A FKBP11 SERPINB1 STK17A CCR7 PTPRCAP +CD56+ NK CST7 SPON2 HOPX GNLY NKG7 CTSW KLRC2 CD7 MATK PCIF1 CLIC3 FGFBP2 SYPL1 GZMB C9orf142 PRF1 CD247 HCST GZMA GZMH STMN1 ALOX5AP CD63 CD99 IGFBP7 GZMM CCL5 B2M DENND2D GIMAP7 RARRES3 SIT1 IFITM1 PFN1 EXOG XBP1 IFITM2 GIMAP4 VIMP STK17A LCK GZMK SEPT1 SSR3 CD8A CD3G SPOCK2 RPS3 LDHB IL32 +CD8+ Cytotoxic T FAM101B ADTRP GZMK HCST LAT EGR1 CD8B CCL5 RPL3 LINC00402 FGFBP2 GZMM RPS3 CD3E GYPC DENND2D C9orf142 GZMA SEPT1 JUN FYB CD8A SELL ALOX5AP CD3G STK17A AQP3 C1orf228 CD3D HOPX NKG7 CD2 NGFRAP1 RPLP1 RPSA CCR7 IL7R SPON2 PRF1 RARRES3 PRKCQ-AS1 FKBP11 MANF CTSW GNLY CD27 LDHB MAL LTB RPLP0 +CD8+/CD45RA+ Naive Cytotoxic RP11-291B21.2 CD8A CD8B RSBN1L-AS1 GIMAP5 GZMM GALE CCR7 STK17A RAB3IP GZMH GIMAP7 CD3E C1orf228 LCK CCL5 PEBP1 CD27 GYPC LDHB RNF34 CD99 CD3G PFN1 IL7R CD2 C9orf142 TMSB10 NGFRAP1 S1PR4 ITM2A CD7 RPS3 IL32 FYB IFITM1 CD52 LAT GIMAP4 MAL STMN1 NOSIP RARRES3 SPOCK2 ACTG1 PRF1 CD3D RPLP1 SELL GZMA +Dendritic HLA-DQB1 CST3 HLA-DRB1 HLA-DQA2 HLA-DQA1 LYZ HLA-DPB1 HLA-DPA1 HLA-DMA HLA-DRA VIM CD74 ALDH2 FCER1A GPX1 HLA-DRB5 LGALS2 MNDA FCGRT GRN HLA-DMB FOS CPVL CLEC10A AMICA1 CFP LY86 GSTP1 RP11-473M20.7 IL1B GSN SPINT2 CCDC163P IGFBP7 EXOG DUSP1 CD63 COTL1 FTH1 SPI1 TYROBP SPIB S100A11 OAZ1 CTSS CCDC50 AIF1 SERPINB1 TMSB10 PCIF1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/marker_2.tsv Thu May 30 11:10:21 2024 +0000 @@ -0,0 +1,8 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 +0 IL32 SEPT1 LCK CD3D CD3G STMN1 CD247 CD3E CD2 LAT GIMAP7 CD99 PFN1 ACTG1 SPOCK2 AES CD7 CD52 CCR7 HCST GIMAP4 GZMM HOPX SIT1 GZMK C9orf142 ALOX5AP RARRES3 LDHB DENND2D ARHGDIB CST7 B2M FYB LINC00402 TMSB10 S1PR4 MAL CD27 IFITM1 GYPC NOSIP RPSA CCL5 PRF1 SPON2 SELL KLRC2 STK17A CD8A +1 PILRA OAZ1 FTL FCGR3A PSAP CD68 CEBPB LST1 FCN1 FCER1G FTH1 SERPINA1 AIF1 TMEM176B NPC2 CTSS TYROBP SAT1 S100A11 HCK MS4A7 CFD COTL1 RP11-290F20.3 IFITM3 DUSP1 STXBP2 IFITM2 SPI1 S100A4 MPP1 GALE SESN2 CCDC163P RSBN1L-AS1 ADTRP CORO1B RP11-390E23.6 CFP MNDA VIMP CHD4 GSTP1 FCGRT ARHGDIB PFN1 CST3 GRN SERPINB1 HLA-DRB5 +2 FCER1A ALDH2 HLA-DQA1 AMICA1 HLA-DQB1 LYZ CLEC10A HLA-DQA2 GPX1 HLA-DRA HLA-DRB1 HLA-DMA LGALS2 FOS HLA-DPB1 CD74 HLA-DRB5 CST3 GRN HLA-DPA1 HLA-DMB FCGRT IL1B GSN RP11-473M20.7 MNDA VIM CFP CD63 IGFBP7 LY86 GSTP1 EXOG SPIB SPINT2 TMSB10 PCIF1 CCDC50 S100A4 COTL1 SPI1 ETV2 DUSP1 RPLP0 TYROBP RP3-467N11.1 ALOX5AP PEBP1 S100A11 RAB3IP +3 CD79B PNOC CCDC50 BANK1 MS4A1 KIAA0125 NCF1 FAM63B BLK SMARCB1 PTPRCAP PDLIM1 CD79A TSHZ2 MPHOSPH9 SPIB SELL TNFRSF13B AL928768.3 HLA-DMB CD52 GYPC FCRLA RPL3 LY9 BTG1 TPD52 LTB RPLP1 ARHGDIB CD74 POU2AF1 RPSA HCST SPOCK2 SIT1 LY86 EXOG TNFRSF17 HLA-DRA PEBP1 PLAC8 ACTG1 RPS3 SEPT1 HLA-DPA1 SSR3 RPLP0 HLA-DPB1 H1FX +4 CPVL VIM HLA-DPA1 GSTP1 CST3 LY86 HMGA1 FCGRT RAB3IP CD74 HLA-DPB1 HLA-DMA SPINT2 HLA-DRB1 HLA-DQB1 SERPINB1 H1FX HLA-DRB5 HLA-DRA HLA-DQA2 LYZ RNF34 ACTG1 EXOG SAT1 GALE CALR CTSS SPI1 FTH1 GNG7 HLA-DMB HLA-DQA1 PCIF1 GRN LGALS2 NPC2 GPX1 IGFBP7 COTL1 CFD GYPC RP11-290F20.3 ALDH2 STXBP2 DUSP1 FCGR3A AIF1 MS4A7 CD63 +5 DERL3 TNFRSF17 MZB1 XBP1 FKBP11 IGJ SSR4 UBE2J1 SUB1 ISG20 IGLL5 GNG7 SSR3 POU2AF1 VIMP CALR PEBP1 CCDC132 EAF2 CD79A AL928768.3 MANF TPD52 TNFRSF13B JUN CD27 SMARCB1 NUCB2 ADTRP ATXN7L3B RP3-467N11.1 PCIF1 CDK6 S1PR4 AQP3 GYPC NCF1 CD99 FCRLA TMSB10 B2M RARRES3 RPLP1 RPLP0 CD52 ITM2A GPX1 HCST CCDC50 RP11-620J15.3 +6 PRSS57 SPINK2 C19orf77 RP11-620J15.3 SNHG7 CYTL1 EGFL7 RP3-467N11.1 NGFRAP1 EGR1 CDK6 SOX4 NFE2 H1FX SERPINB1 SPINT2 HMGA1 RPLP0 ATXN7L3B NUCB2 IGFBP7 IL1B SYPL1 RPLP1 C1orf228 FAM101B RPS3 RPL3 CD63 MATK KIAA0125 PRKCQ-AS1 LDHB SEPT1 SPON2 JUN PEBP1 ITM2A SELL SSR3 XBP1 GYPC UBE2J1 STK17A VIMP STMN1 HOPX VIM MZB1 CD99
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/marker_3.tsv Thu May 30 11:10:21 2024 +0000 @@ -0,0 +1,11 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 +CD14+ Monocyte PILRA PSAP CD68 TMEM176B FTL NPC2 LST1 FCGR3A FCER1G CEBPB FCN1 SERPINA1 OAZ1 CFD FTH1 HCK AIF1 SAT1 CTSS S100A11 MS4A7 TYROBP COTL1 STXBP2 RP11-290F20.3 S100A4 IFITM2 SPI1 DUSP1 SESN2 IFITM3 MPP1 GALE CORO1B RP11-390E23.6 VIMP RSBN1L-AS1 CHD4 CFP GSTP1 PFN1 FCGRT ADTRP ARHGDIB AMICA1 HLA-DRB5 CST3 GRN HLA-DPA1 SSR3 +CD19+ B TNFRSF13B CD79B SMARCB1 PNOC CCDC50 AL928768.3 BANK1 MS4A1 CD79A ISG20 IGLL5 TNFRSF17 KIAA0125 TPD52 PEBP1 FKBP11 CCDC132 SUB1 POU2AF1 MZB1 PTPRCAP UBE2J1 BLK SPIB DERL3 FAM63B MPHOSPH9 IGJ FCRLA XBP1 NCF1 SSR3 CD52 TSHZ2 PDLIM1 VIMP SSR4 S1PR4 SELL HMGA1 NUCB2 JUN CD27 ARHGDIB GYPC CALR ADTRP BTG1 EXOG RARRES3 +CD34+ PRSS57 C19orf77 SPINK2 RP11-620J15.3 SNHG7 CYTL1 EGFL7 NGFRAP1 SOX4 NFE2 EGR1 RP3-467N11.1 H1FX CDK6 SERPINB1 SPINT2 HMGA1 IL1B NUCB2 RPLP0 IGFBP7 RPLP1 ATXN7L3B RPS3 C1orf228 KIAA0125 RPL3 SYPL1 CD63 LDHB SEPT1 JUN FAM101B PRKCQ-AS1 MATK PEBP1 SELL ITM2A SSR3 SPON2 XBP1 UBE2J1 VIMP GYPC STK17A STMN1 VIM MZB1 HOPX CD99 +CD4+/CD25 T Reg IL32 SPOCK2 ACTG1 CD2 CD3D GPR171 ARHGDIB ACOX1 MAL SIT1 GIMAP4 AES CD52 SEPT1 TMSB10 LAT STMN1 LINC00402 CD27 TSHZ2 S1PR4 CD3E PFN1 CD99 AQP3 PTPRCAP CD3G LY9 LCK CD247 S100A4 CCR7 TTC39C CORO1B MPHOSPH9 FYB RPSA FLT3LG B2M GIMAP7 PRKCQ-AS1 SELL BTG1 CCDC132 GYPC DENND2D LDHB IL7R ITM2A RPLP0 +CD4+/CD45RA+/CD25- Naive T EAF2 GNG7 SSR4 CALR DERL3 MANF IGJ XBP1 ATXN7L3B SSR3 UBE2J1 CD79A MZB1 RP3-467N11.1 TNFRSF17 NCF1 CDK6 SUB1 POU2AF1 AL928768.3 FKBP11 VIMP GYPC JUN CD27 PEBP1 SMARCB1 FLT3LG RPLP1 RPLP0 CCDC50 ISG20 IGLL5 HCST GSTP1 GPX1 CD52 VIM PTPRCAP FCGRT CD74 B2M RPL3 CYTL1 SPINK2 PRSS57 C19orf77 RP11-620J15.3 FAM101B CCDC132 +CD4+/CD45RO+ Memory RNF138 NOSIP IFITM1 LCK RARRES3 ALOX5AP FAM63B RAB3IP GZMK CD3G SEPT1 LDHB SELL CD3D EXOG RPSA CD247 AES CD52 TMSB10 NUCB2 DENND2D RPL3 RPLP1 ACTG1 FYB GIMAP7 CORO1B LY9 CD7 PFN1 RPS3 GYPC CD2 ARHGDIB IL32 RPLP0 CD99 CD3E GIMAP4 HCST B2M LAT ISG20 ITM2A FKBP11 SERPINB1 STK17A CCR7 PTPRCAP +CD56+ NK CST7 SPON2 HOPX GNLY NKG7 CTSW KLRC2 CD7 MATK PCIF1 CLIC3 FGFBP2 SYPL1 GZMB C9orf142 PRF1 CD247 HCST GZMA GZMH STMN1 ALOX5AP CD63 CD99 IGFBP7 GZMM CCL5 B2M DENND2D GIMAP7 RARRES3 SIT1 IFITM1 PFN1 EXOG XBP1 IFITM2 GIMAP4 VIMP STK17A LCK GZMK SEPT1 SSR3 CD8A CD3G SPOCK2 RPS3 LDHB IL32 +CD8+ Cytotoxic T FAM101B ADTRP GZMK HCST LAT EGR1 CD8B CCL5 RPL3 LINC00402 FGFBP2 GZMM RPS3 CD3E GYPC DENND2D C9orf142 GZMA SEPT1 JUN FYB CD8A SELL ALOX5AP CD3G STK17A AQP3 C1orf228 CD3D HOPX NKG7 CD2 NGFRAP1 RPLP1 RPSA CCR7 IL7R SPON2 PRF1 RARRES3 PRKCQ-AS1 FKBP11 MANF CTSW GNLY CD27 LDHB MAL LTB RPLP0 +CD8+/CD45RA+ Naive Cytotoxic RP11-291B21.2 CD8A CD8B RSBN1L-AS1 GIMAP5 GZMM GALE CCR7 STK17A RAB3IP GZMH GIMAP7 CD3E C1orf228 LCK CCL5 PEBP1 CD27 GYPC LDHB RNF34 CD99 CD3G PFN1 IL7R CD2 C9orf142 TMSB10 NGFRAP1 S1PR4 ITM2A CD7 RPS3 IL32 FYB IFITM1 CD52 LAT GIMAP4 MAL STMN1 NOSIP RARRES3 SPOCK2 ACTG1 PRF1 CD3D RPLP1 SELL GZMA +Dendritic HLA-DQB1 CST3 HLA-DRB1 HLA-DQA2 HLA-DQA1 LYZ HLA-DPB1 HLA-DPA1 HLA-DMA HLA-DRA VIM CD74 ALDH2 FCER1A GPX1 HLA-DRB5 LGALS2 MNDA FCGRT GRN HLA-DMB FOS CPVL CLEC10A AMICA1 CFP LY86 GSTP1 RP11-473M20.7 IL1B GSN SPINT2 CCDC163P IGFBP7 EXOG DUSP1 CD63 COTL1 FTH1 SPI1 TYROBP SPIB S100A11 OAZ1 CTSS CCDC50 AIF1 SERPINB1 TMSB10 PCIF1