|
Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4 |
|
added:
sc3-estimate-k.xml sc3-macros.xml test-data/barcodes.tsv test-data/genes.tsv test-data/pbmc3k.rds test-data/pbmc3k_filtered_gene_bc_matrices.tar.gz test-data/pbmc3k_sc3.rds test-data/scater_log.rds test-data/test |
| b |
| diff -r 000000000000 -r aab4d3a52ee3 sc3-estimate-k.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sc3-estimate-k.xml Wed Apr 03 11:25:01 2019 -0400 |
| [ |
| @@ -0,0 +1,41 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="sc3_estimate_k" name="SC3 Estimate" version="@TOOL_VERSION@+galaxy0"> + <description>the number of clusters for k-means clustering</description> + <macros> + <import>sc3-macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +sc3-sc3-estimate-k.R -i '${sc3_prepared}' -t '${sc3_estimated_k}' -o sc3_estimated.rds && + +echo -n "estimated k = " && cat ${sc3_estimated_k} + ]]></command> + + <inputs> + <param type="data" name="sc3_prepared" format="rdata" label="Serialised sc3 SingleCellExperiment object"/> + </inputs> + + <outputs> + <data name="sc3_estimated_k" format="txt" label="${tool.name} on ${on_string}: txt file containting estimated K value"/> + </outputs> + + <tests> + <test> + <param name="sc3_prepared" value="sc3_prepared.rds"/> + <output name="sc3_estimated_k" file="sc3-estimated-k.txt"/> + </test> + </tests> + + <help><![CDATA[ +======================================================================================== +Uses Tracy-Widom theory on random matrices to estimate the optimal number of clusters k. +======================================================================================== + +It creates and populates the k_estimation item of the sc3 slot of the metadata(object). + +@HELP@ + +@VERSION_HISTORY@ + ]]></help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r aab4d3a52ee3 sc3-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sc3-macros.xml Wed Apr 03 11:25:01 2019 -0400 |
| [ |
| @@ -0,0 +1,31 @@ +<macros> + <token name="@TOOL_VERSION@">1.8.0</token> + <token name="@HELP@">Documentation can be found at http://bioconductor.org/packages/release/bioc/vignettes/SC3/inst/doc/SC3.html</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.0.4">sc3-scripts</requirement> + <yield/> + </requirements> + </xml> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +1.8.0+galaxy0: Initial contribution. Ni Huang and Carlos Talavera-Lopez, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute. + ]]></token> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nmeth.4236</citation> + <citation type="bibtex"> + @misc{githubbioconductor-sc3-scripts.git, + author = {Jonathan Manning, Ni Huang, Jean Chang, Carlos Talavera-López, EBI Gene Expression Team}, + year = {2018}, + title = {SC3-scripts: command line interface for SC3}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts.git}, + }</citation> + <yield /> + </citations> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r aab4d3a52ee3 test-data/barcodes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcodes.tsv Wed Apr 03 11:25:01 2019 -0400 |
| b |
| b'@@ -0,0 +1,2700 @@\n+AAACATACAACCAC-1\n+AAACATTGAGCTAC-1\n+AAACATTGATCAGC-1\n+AAACCGTGCTTCCG-1\n+AAACCGTGTATGCG-1\n+AAACGCACTGGTAC-1\n+AAACGCTGACCAGT-1\n+AAACGCTGGTTCTT-1\n+AAACGCTGTAGCCA-1\n+AAACGCTGTTTCTG-1\n+AAACTTGAAAAACG-1\n+AAACTTGATCCAGA-1\n+AAAGAGACGAGATA-1\n+AAAGAGACGCGAGA-1\n+AAAGAGACGGACTT-1\n+AAAGAGACGGCATT-1\n+AAAGATCTGGGCAA-1\n+AAAGCAGAAGCCAT-1\n+AAAGCAGATATCGG-1\n+AAAGCCTGTATGCG-1\n+AAAGGCCTGTCTAG-1\n+AAAGTTTGATCACG-1\n+AAAGTTTGGGGTGA-1\n+AAAGTTTGTAGAGA-1\n+AAAGTTTGTAGCGT-1\n+AAATCAACAATGCC-1\n+AAATCAACACCAGT-1\n+AAATCAACCAGGAG-1\n+AAATCAACCCTATT-1\n+AAATCAACGGAAGC-1\n+AAATCAACTCGCAA-1\n+AAATCATGACCACA-1\n+AAATCCCTCCACAA-1\n+AAATCCCTGCTATG-1\n+AAATGTTGAACGAA-1\n+AAATGTTGCCACAA-1\n+AAATGTTGTGGCAT-1\n+AAATTCGAAGGTTC-1\n+AAATTCGAATCACG-1\n+AAATTCGAGCTGAT-1\n+AAATTCGAGGAGTG-1\n+AAATTCGATTCTCA-1\n+AAATTGACACGACT-1\n+AAATTGACTCGCTC-1\n+AACAAACTCATTTC-1\n+AACAAACTTTCGTT-1\n+AACAATACGACGAG-1\n+AACACGTGCAGAGG-1\n+AACACGTGGAAAGT-1\n+AACACGTGGAACCT-1\n+AACACGTGGCTACA-1\n+AACACGTGTACGAC-1\n+AACAGCACAAGAGT-1\n+AACATTGATGGGAG-1\n+AACCAGTGATACCG-1\n+AACCCAGATCGCTC-1\n+AACCGATGCTCCCA-1\n+AACCGATGGTCATG-1\n+AACCGATGTTCTAC-1\n+AACCGCCTAGCGTT-1\n+AACCGCCTCTACGA-1\n+AACCTACTGTGAGG-1\n+AACCTACTGTGTTG-1\n+AACCTTACGAGACG-1\n+AACCTTACGCGAGA-1\n+AACCTTACTAACGC-1\n+AACCTTTGGACGGA-1\n+AACCTTTGTACGCA-1\n+AACGCAACAAGTAG-1\n+AACGCATGACCCAA-1\n+AACGCATGCCTTCG-1\n+AACGCATGTACTTC-1\n+AACGCCCTCGGGAA-1\n+AACGCCCTCGTACA-1\n+AACGCCCTGCTTAG-1\n+AACGCCCTGGCATT-1\n+AACGTCGAGTATCG-1\n+AACGTGTGAAAGCA-1\n+AACGTGTGGCGGAA-1\n+AACGTGTGTCCAAG-1\n+AACGTGTGTGCTTT-1\n+AACTACCTTAGAGA-1\n+AACTCACTCAAGCT-1\n+AACTCACTTGGAGG-1\n+AACTCGGAAAGTGA-1\n+AACTCGGAAGGTCT-1\n+AACTCTTGCAGGAG-1\n+AACTGTCTCCCTTG-1\n+AACTTGCTACGCTA-1\n+AACTTGCTGGGACA-1\n+AAGAACGAGTGTTG-1\n+AAGAAGACGTAGGG-1\n+AAGACAGAAGTCTG-1\n+AAGACAGAGGATCT-1\n+AAGACAGATTACCT-1\n+AAGAGATGGGTAGG-1\n+AAGATGGAAAACAG-1\n+AAGATGGAGAACTC-1\n+AAGATGGAGATAAG-1\n+AAGATTACAACCTG-1\n+AAGATTACAGATCC-1\n+AAGATTACCCGTTC-1\n+AAGATTACCGCCTT-1\n+AAGATTACCTCAAG-1\n+AAGATTACTCCTCG-1\n+AAGCAAGAGCGAGA-1\n+AAGCAAGAGCTTAG-1\n+AAGCAAGAGGTGTT-1\n+AAGCACTGAGCAAA-1\n+AAGCACTGCATACG-1\n+AAGCACTGGTTCTT-1\n+AAGCCAACGTGTTG-1\n+AAGCCATGAACTGC-1\n+AAGCCATGACACGT-1\n+AAGCCATGCGTGAT-1\n+AAGCCATGTCTCGC-1\n+AAGCCTGACATGCA-1\n+AAGCCTGACCGAAT-1\n+AAGCGACTCCTCAC-1\n+AAGCGACTGTGTCA-1\n+AAGCGACTTACAGC-1\n+AAGCGACTTTGACG-1\n+AAGCGTACGTCTTT-1\n+AAGGCTTGCGAACT-1\n+AAGGTCACGGTTAC-1\n+AAGGTCACTGTTTC-1\n+AAGGTCACTTCCCG-1\n+AAGGTCTGACAGTC-1\n+AAGGTCTGCAGATC-1\n+AAGGTCTGGTATGC-1\n+AAGTAACTCTGAAC-1\n+AAGTAACTGAGATA-1\n+AAGTAGGATACAGC-1\n+AAGTATACCGAACT-1\n+AAGTCCGACTTGTT-1\n+AAGTCCGATAGAAG-1\n+AAGTCTCTAGTCGT-1\n+AAGTCTCTCGGAGA-1\n+AAGTGGCTTGGAGG-1\n+AAGTTCCTCATTCT-1\n+AAGTTCCTTCTTAC-1\n+AATAAGCTCGAATC-1\n+AATAAGCTCGTTGA-1\n+AATACCCTGGACGA-1\n+AATACCCTGGCATT-1\n+AATACTGAAAGGGC-1\n+AATACTGAATTGGC-1\n+AATAGGGAACCCTC-1\n+AATAGGGAGAATGA-1\n+AATCAAACTATCGG-1\n+AATCCGGAATGCTG-1\n+AATCCTACCGGTAT-1\n+AATCCTTGACGGGA-1\n+AATCCTTGGTGAGG-1\n+AATCGGTGGAACTC-1\n+AATCGGTGTGCTTT-1\n+AATCTAGAAAAGTG-1\n+AATCTAGAATCGGT-1\n+AATCTCACAGCCTA-1\n+AATCTCACTCTAGG-1\n+AATCTCTGAACAGA-1\n+AATCTCTGCTTTAC-1\n+AATGATACACCAAC-1\n+AATGATACGGTCAT-1\n+AATGCGTGACACCA-1\n+AATGCGTGGACGGA-1\n+AATGCGTGGCTATG-1\n+AATGGAGAATCGTG-1\n+AATGGAGATCCTTA-1\n+AATGGCTGACACCA-1\n+AATGGCTGCGTGAT-1\n+AATGGCTGTAAAGG-1\n+AATGGCTGTACTCT-1\n+AATGGCTGTGAAGA-1\n+AATGTAACGGTGGA-1\n+AATGTAACGTTTGG-1\n+AATGTCCTCTTCTA-1\n+AATGTTGACAGTCA-1\n+AATGTTGAGTTGAC-1\n+AATGTTGATCTACT-1\n+AATTACGAATTCCT-1\n+AATTACGACTTCTA-1\n+AATTACGAGTAGCT-1\n+AATTACGAGTGAGG-1\n+AATTACGATTGGCA-1\n+AATTCCTGCTCAGA-1\n+AATTGATGTCGCAA-1\n+AATTGTGACTTGGA-1\n+ACAAAGGAGGGTGA-1\n+ACAAATTGATTCTC-1\n+ACAAATTGCTCAGA-1\n+ACAAATTGTTGCGA-1\n+ACAACCGAGGGATG-1\n+ACAACCGAGTTACG-1\n+ACAAGAGAAGTCGT-1\n+ACAAGAGACTTATC-1\n+ACAAGAGAGTTGAC-1\n+ACAATCCTAACCGT-1\n+ACAATCCTTAGCGT-1\n+ACAATTGACTGACA-1\n+ACAATTGATGACTG-1\n+ACACAGACACCTGA-1\n+ACACAGACCATACG-1\n+ACACCAGAGGGCAA-1\n+ACACCCTGGTGTTG-1\n+ACACGAACAGTTCG-1\n+ACACGATGACGCAT-1\n+ACACGATGATGTGC-1\n+ACACGATGTCGTAG-1\n+ACACGATGTGGTCA-1\n+ACAGACACGGCATT-1\n+ACAGACACGTTGTG-1\n+ACAGCAACACCTAG-1\n+ACAGCAACCTCAAG-1\n+ACAGGTACCCCACT-1\n+ACAGGTACGCTGTA-1\n+ACAGGTACTGGTGT-1\n+ACAGTCGACCCAAA-1\n+ACAGTCGACCGATA-1\n+ACAGTGACTCACCC-1\n+ACAGTGACTCTATC-1\n+A'..b'-1\n+TGCTATACTGCTGA-1\n+TGCTGAGAGAGCAG-1\n+TGCTGAGATTATCC-1\n+TGGAAAGACTCTCG-1\n+TGGAAAGAGCGATT-1\n+TGGAAAGAGGTCAT-1\n+TGGAAAGATATGGC-1\n+TGGAACACAAACAG-1\n+TGGAACACGCTAAC-1\n+TGGAAGCTCAGATC-1\n+TGGACCCTACACTG-1\n+TGGACCCTCATGGT-1\n+TGGACCCTGGTACT-1\n+TGGACTGAGTATGC-1\n+TGGAGACTATCAGC-1\n+TGGAGACTGAAACA-1\n+TGGAGACTTCAAGC-1\n+TGGAGACTTGACCA-1\n+TGGAGGGACGGAGA-1\n+TGGAGGGAGCTATG-1\n+TGGATCGATAAAGG-1\n+TGGATGTGACCTAG-1\n+TGGATGTGATGTCG-1\n+TGGATGTGTGAAGA-1\n+TGGATTCTCATACG-1\n+TGGCAATGCTTGTT-1\n+TGGCAATGGAGGGT-1\n+TGGCACCTTCACGA-1\n+TGGCACCTTCAGTG-1\n+TGGGTATGAAGAGT-1\n+TGGGTATGCACAAC-1\n+TGGGTATGGTACGT-1\n+TGGGTATGTTTGGG-1\n+TGGTAGACATGCCA-1\n+TGGTAGACCCTCAC-1\n+TGGTAGACCTGATG-1\n+TGGTAGTGCACTGA-1\n+TGGTATCTAAACAG-1\n+TGGTATCTCTTCCG-1\n+TGGTCAGACCCAAA-1\n+TGGTCAGACCGTTC-1\n+TGGTTACTGACGTT-1\n+TGGTTACTGTTCTT-1\n+TGTAACCTAGAGGC-1\n+TGTAACCTTGCCTC-1\n+TGTAATGACACAAC-1\n+TGTAATGAGGTAAA-1\n+TGTACTTGCTCTAT-1\n+TGTAGGTGCGAGAG-1\n+TGTAGGTGCTATGG-1\n+TGTAGGTGCTCTAT-1\n+TGTAGGTGTGCTGA-1\n+TGTAGTCTTCCAGA-1\n+TGTAGTCTTGCACA-1\n+TGTATCTGTTAGGC-1\n+TGTATGCTCATGGT-1\n+TGTATGCTGTAGGG-1\n+TGTATGCTTTCATC-1\n+TGTCAGGAATACCG-1\n+TGTCAGGAGATGAA-1\n+TGTCTAACCCCTTG-1\n+TGTGACGATTCTCA-1\n+TGTGAGACTGTCAG-1\n+TGTGAGACTTGAGC-1\n+TGTGAGTGACCACA-1\n+TGTGAGTGAGTGCT-1\n+TGTGAGTGGAGATA-1\n+TGTGATCTCTCTAT-1\n+TGTGATCTGACACT-1\n+TGTGGATGGCCAAT-1\n+TGTTAAGACAAAGA-1\n+TGTTAAGATAAGGA-1\n+TGTTAAGATTGGCA-1\n+TGTTACACCGCATA-1\n+TGTTACACGACTAC-1\n+TGTTACTGGCTACA-1\n+TGTTACTGTAGTCG-1\n+TTAACCACCGTAAC-1\n+TTAACCACTAAGGA-1\n+TTAACCACTCAGAC-1\n+TTACACACGTGTTG-1\n+TTACACACTCCTAT-1\n+TTACCATGAATCGC-1\n+TTACCATGGTTGAC-1\n+TTACCATGTGTCTT-1\n+TTACCATGTTGTGG-1\n+TTACGACTGAGAGC-1\n+TTACGACTTGACAC-1\n+TTACGTACGTTCAG-1\n+TTACTCGAACGTTG-1\n+TTACTCGAAGAATG-1\n+TTACTCGACGCAAT-1\n+TTACTCGAGGGTGA-1\n+TTACTCGATCTACT-1\n+TTAGAATGTGGTGT-1\n+TTAGAATGTGTAGC-1\n+TTAGACCTCCTACC-1\n+TTAGACCTCCTTTA-1\n+TTAGCTACAACCGT-1\n+TTAGCTACTGTCCC-1\n+TTAGCTACTTTCGT-1\n+TTAGGGACGCGAAG-1\n+TTAGGGTGCTGGAT-1\n+TTAGGGTGTCCTGC-1\n+TTAGGTCTACTTTC-1\n+TTAGTCACCAGTTG-1\n+TTAGTCTGAAAGCA-1\n+TTAGTCTGCCAACA-1\n+TTAGTCTGTGCACA-1\n+TTATCCGACTAGTG-1\n+TTATCCGAGAAAGT-1\n+TTATGAGAGATAAG-1\n+TTATGCACGTCACA-1\n+TTATGGCTTATGGC-1\n+TTATTCCTATGCTG-1\n+TTATTCCTGGACAG-1\n+TTATTCCTGGTACT-1\n+TTATTCCTTCGTGA-1\n+TTCAAAGATAAAGG-1\n+TTCAACACAACAGA-1\n+TTCAACACCCCAAA-1\n+TTCAACACGGACGA-1\n+TTCAAGCTAAGAAC-1\n+TTCAAGCTAGATGA-1\n+TTCAAGCTGTTGAC-1\n+TTCAAGCTTCCAAG-1\n+TTCAAGCTTGATGC-1\n+TTCAAGCTTTCGCC-1\n+TTCACAACCCGTTC-1\n+TTCACAACGTCTGA-1\n+TTCAGACTACCCAA-1\n+TTCAGACTCTCGAA-1\n+TTCAGTACCGACTA-1\n+TTCAGTACTCAAGC-1\n+TTCAGTACTCCTAT-1\n+TTCAGTTGCCAAGT-1\n+TTCAGTTGTCCTTA-1\n+TTCAGTTGTCTAGG-1\n+TTCAGTTGTCTCGC-1\n+TTCATCGAGGTGGA-1\n+TTCATGTGTGGTGT-1\n+TTCATTCTATGTCG-1\n+TTCATTCTTCTCTA-1\n+TTCCAAACCTATGG-1\n+TTCCAAACCTCCCA-1\n+TTCCAAACTCCCAC-1\n+TTCCAAACTTGACG-1\n+TTCCATGACGAGAG-1\n+TTCCATGACTGTCC-1\n+TTCCCACTTGAGGG-1\n+TTCCCACTTGTCTT-1\n+TTCCTAGAAAGTGA-1\n+TTCCTAGACTAGTG-1\n+TTCGAGGACTCTAT-1\n+TTCGAGGAGGGCAA-1\n+TTCGAGGATAGAAG-1\n+TTCGATTGAGCATC-1\n+TTCGGAGAATGCCA-1\n+TTCGGAGATGTGCA-1\n+TTCGTATGAAAAGC-1\n+TTCGTATGGATAGA-1\n+TTCGTATGGTCTGA-1\n+TTCGTATGTCCTTA-1\n+TTCTACGAACGTAC-1\n+TTCTACGAGTTGGT-1\n+TTCTAGTGACACGT-1\n+TTCTAGTGCATGAC-1\n+TTCTAGTGGAGAGC-1\n+TTCTAGTGGTCACA-1\n+TTCTCAGAAGAGAT-1\n+TTCTCAGAAGCATC-1\n+TTCTCAGATGGAGG-1\n+TTCTGATGGAGACG-1\n+TTCTTACTCTGGAT-1\n+TTGAACCTCCTTGC-1\n+TTGAATGAACTACG-1\n+TTGAATGACTTACT-1\n+TTGAATGATCTCAT-1\n+TTGACACTCTGTAG-1\n+TTGACACTGATAAG-1\n+TTGAGGACAGAACA-1\n+TTGAGGACTACGCA-1\n+TTGAGGTGGACGGA-1\n+TTGCATTGAGCTAC-1\n+TTGCATTGCTAAGC-1\n+TTGCATTGTGACTG-1\n+TTGCTAACACCAAC-1\n+TTGCTAACACGCTA-1\n+TTGCTAACCACTCC-1\n+TTGCTATGGTACGT-1\n+TTGCTATGGTAGGG-1\n+TTGGAGACCAATCG-1\n+TTGGAGACGCTATG-1\n+TTGGAGACTATGGC-1\n+TTGGGAACTGAACC-1\n+TTGGTACTACTGGT-1\n+TTGGTACTCTTAGG-1\n+TTGGTACTGAATCC-1\n+TTGGTACTGGATTC-1\n+TTGTACACGTTGTG-1\n+TTGTACACTTGCAG-1\n+TTGTAGCTAGCTCA-1\n+TTGTAGCTCTCTTA-1\n+TTGTCATGGACGGA-1\n+TTTAGAGATCCTCG-1\n+TTTAGCTGATACCG-1\n+TTTAGCTGGATACC-1\n+TTTAGCTGTACTCT-1\n+TTTAGGCTCCTTTA-1\n+TTTATCCTGTTGTG-1\n+TTTCACGAGGTTCA-1\n+TTTCAGTGGAAGGC-1\n+TTTCAGTGTCACGA-1\n+TTTCAGTGTCTATC-1\n+TTTCAGTGTGCAGT-1\n+TTTCCAGAGGTGAG-1\n+TTTCGAACACCTGA-1\n+TTTCGAACTCTCAT-1\n+TTTCTACTGAGGCA-1\n+TTTCTACTTCCTCG-1\n+TTTGCATGAGAGGC-1\n+TTTGCATGCCTCAC-1\n' |
| b |
| diff -r 000000000000 -r aab4d3a52ee3 test-data/genes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes.tsv Wed Apr 03 11:25:01 2019 -0400 |
| b |
| b'@@ -0,0 +1,32738 @@\n+ENSG00000243485\tMIR1302-10\n+ENSG00000237613\tFAM138A\n+ENSG00000186092\tOR4F5\n+ENSG00000238009\tRP11-34P13.7\n+ENSG00000239945\tRP11-34P13.8\n+ENSG00000237683\tAL627309.1\n+ENSG00000239906\tRP11-34P13.14\n+ENSG00000241599\tRP11-34P13.9\n+ENSG00000228463\tAP006222.2\n+ENSG00000237094\tRP4-669L17.10\n+ENSG00000235249\tOR4F29\n+ENSG00000236601\tRP4-669L17.2\n+ENSG00000236743\tRP5-857K21.15\n+ENSG00000231709\tRP5-857K21.1\n+ENSG00000235146\tRP5-857K21.2\n+ENSG00000239664\tRP5-857K21.3\n+ENSG00000230021\tRP5-857K21.4\n+ENSG00000223659\tRP5-857K21.5\n+ENSG00000185097\tOR4F16\n+ENSG00000235373\tRP11-206L10.3\n+ENSG00000240618\tRP11-206L10.5\n+ENSG00000229905\tRP11-206L10.4\n+ENSG00000228327\tRP11-206L10.2\n+ENSG00000237491\tRP11-206L10.9\n+ENSG00000269831\tAL669831.1\n+ENSG00000177757\tFAM87B\n+ENSG00000225880\tLINC00115\n+ENSG00000230368\tFAM41C\n+ENSG00000269308\tAL645608.2\n+ENSG00000272438\tRP11-54O7.16\n+ENSG00000230699\tRP11-54O7.1\n+ENSG00000241180\tRP11-54O7.2\n+ENSG00000223764\tRP11-54O7.3\n+ENSG00000187634\tSAMD11\n+ENSG00000268179\tAL645608.1\n+ENSG00000188976\tNOC2L\n+ENSG00000187961\tKLHL17\n+ENSG00000187583\tPLEKHN1\n+ENSG00000187642\tC1orf170\n+ENSG00000272512\tRP11-54O7.17\n+ENSG00000188290\tHES4\n+ENSG00000224969\tRP11-54O7.11\n+ENSG00000187608\tISG15\n+ENSG00000188157\tAGRN\n+ENSG00000273443\tRP11-54O7.18\n+ENSG00000237330\tRNF223\n+ENSG00000131591\tC1orf159\n+ENSG00000223823\tRP11-465B22.5\n+ENSG00000272141\tRP11-465B22.8\n+ENSG00000205231\tTTLL10-AS1\n+ENSG00000162571\tTTLL10\n+ENSG00000186891\tTNFRSF18\n+ENSG00000186827\tTNFRSF4\n+ENSG00000078808\tSDF4\n+ENSG00000176022\tB3GALT6\n+ENSG00000184163\tFAM132A\n+ENSG00000260179\tRP5-902P8.12\n+ENSG00000160087\tUBE2J2\n+ENSG00000230415\tRP5-902P8.10\n+ENSG00000162572\tSCNN1D\n+ENSG00000131584\tACAP3\n+ENSG00000169972\tPUSL1\n+ENSG00000127054\tCPSF3L\n+ENSG00000224051\tGLTPD1\n+ENSG00000169962\tTAS1R3\n+ENSG00000107404\tDVL1\n+ENSG00000162576\tMXRA8\n+ENSG00000175756\tAURKAIP1\n+ENSG00000221978\tCCNL2\n+ENSG00000224870\tRP4-758J18.2\n+ENSG00000242485\tMRPL20\n+ENSG00000272455\tRP4-758J18.13\n+ENSG00000235098\tANKRD65\n+ENSG00000225905\tRP4-758J18.7\n+ENSG00000205116\tTMEM88B\n+ENSG00000225285\tRP4-758J18.10\n+ENSG00000179403\tVWA1\n+ENSG00000215915\tATAD3C\n+ENSG00000160072\tATAD3B\n+ENSG00000197785\tATAD3A\n+ENSG00000205090\tTMEM240\n+ENSG00000160075\tSSU72\n+ENSG00000215014\tAL645728.1\n+ENSG00000228594\tC1orf233\n+ENSG00000272106\tRP11-345P4.9\n+ENSG00000197530\tMIB2\n+ENSG00000189409\tMMP23B\n+ENSG00000248333\tCDK11B\n+ENSG00000272004\tRP11-345P4.10\n+ENSG00000189339\tSLC35E2B\n+ENSG00000269737\tRP11-345P4.7\n+ENSG00000008128\tCDK11A\n+ENSG00000215790\tSLC35E2\n+ENSG00000008130\tNADK\n+ENSG00000078369\tGNB1\n+ENSG00000231050\tRP1-140A9.1\n+ENSG00000169885\tCALML6\n+ENSG00000178821\tTMEM52\n+ENSG00000142609\tC1orf222\n+ENSG00000233542\tRP11-547D24.1\n+ENSG00000187730\tGABRD\n+ENSG00000226969\tRP11-547D24.3\n+ENSG00000067606\tPRKCZ\n+ENSG00000271806\tRP5-892K4.1\n+ENSG00000182873\tRP11-181G12.2\n+ENSG00000162585\tC1orf86\n+ENSG00000269554\tAL590822.2\n+ENSG00000203301\tAL590822.1\n+ENSG00000243558\tRP11-181G12.5\n+ENSG00000234396\tRP11-181G12.4\n+ENSG00000157933\tSKI\n+ENSG00000116151\tMORN1\n+ENSG00000269753\tAL589739.1\n+ENSG00000157916\tRER1\n+ENSG00000157911\tPEX10\n+ENSG00000149527\tPLCH2\n+ENSG00000224387\tRP3-395M20.2\n+ENSG00000229393\tRP3-395M20.3\n+ENSG00000157881\tPANK4\n+ENSG00000197921\tHES5\n+ENSG00000272449\tRP3-395M20.12\n+ENSG00000157873\tTNFRSF14\n+ENSG00000225931\tRP3-395M20.7\n+ENSG00000228037\tRP3-395M20.9\n+ENSG00000157870\tFAM213B\n+ENSG00000142606\tMMEL1\n+ENSG00000237058\tRP13-436F16.1\n+ENSG00000215912\tTTC34\n+ENSG00000233234\tRP11-740P5.2\n+ENSG00000231630\tRP11-740P5.3\n+ENSG00000169717\tACTRT2\n+ENSG00000177133\tLINC00982\n+ENSG00000142611\tPRDM16\n+ENSG00000226286\tRP1-163G9.2\n+ENSG00000272235\tRP11-22L13.1\n+ENSG00000130762\tARHGEF16\n+ENSG00000272088\tRP11-168F9.2\n+ENSG00000162591\tMEGF6\n+ENSG00000238260\tRP11-46F15.2\n+ENSG00000158109\tTPRG1L\n+ENSG00000116213\tWRAP73\n+ENSG00000078900\tTP73\n+ENSG00000227589\tRP5-1092A11.5\n+ENSG00000235131\tRP5-1092A11.2\n+ENSG00000227372\tTP73-AS1\n+ENSG00000162592\tCCDC27\n+ENSG00000235169\tSMIM1\n+ENSG00000130764\tLRRC47\n+ENSG00000272153\tRP1-286D6.5\n+ENSG000'..b'G00000160202\tCRYAA\n+ENSG00000237864\tLINC00322\n+ENSG00000237989\tAP001046.5\n+ENSG00000225637\tAP001046.6\n+ENSG00000142178\tSIK1\n+ENSG00000188660\tLINC00319\n+ENSG00000185186\tLINC00313\n+ENSG00000223975\tAP001048.4\n+ENSG00000160207\tHSF2BP\n+ENSG00000160208\tRRP1B\n+ENSG00000160209\tPDXK\n+ENSG00000160213\tCSTB\n+ENSG00000160214\tRRP1\n+ENSG00000215458\tAP001053.11\n+ENSG00000160216\tAGPAT3\n+ENSG00000160218\tTRAPPC10\n+ENSG00000241945\tPWP2\n+ENSG00000160221\tC21orf33\n+ENSG00000225331\tAP001055.6\n+ENSG00000267913\tAP001055.1\n+ENSG00000237604\tAP001056.1\n+ENSG00000232124\tAP001057.1\n+ENSG00000232698\tAP001058.3\n+ENSG00000160223\tICOSLG\n+ENSG00000142182\tDNMT3L\n+ENSG00000232010\tAP001059.5\n+ENSG00000160224\tAIRE\n+ENSG00000141959\tPFKL\n+ENSG00000160226\tC21orf2\n+ENSG00000184441\tAP001062.7\n+ENSG00000232969\tAP001062.9\n+ENSG00000260256\tAP001063.1\n+ENSG00000142185\tTRPM2\n+ENSG00000230061\tAP001065.2\n+ENSG00000229356\tLRRC3-AS1\n+ENSG00000160233\tLRRC3\n+ENSG00000269430\tLRRC3DN\n+ENSG00000228709\tAP001065.15\n+ENSG00000175894\tTSPEAR\n+ENSG00000235890\tTSPEAR-AS1\n+ENSG00000182912\tC21orf90\n+ENSG00000215455\tKRTAP10-1\n+ENSG00000205445\tKRTAP10-2\n+ENSG00000212935\tKRTAP10-3\n+ENSG00000215454\tKRTAP10-4\n+ENSG00000241123\tKRTAP10-5\n+ENSG00000188155\tKRTAP10-6\n+ENSG00000205441\tKRTAP10-7\n+ENSG00000187766\tKRTAP10-8\n+ENSG00000221837\tKRTAP10-9\n+ENSG00000221859\tKRTAP10-10\n+ENSG00000243489\tKRTAP10-11\n+ENSG00000212933\tKRTAP12-4\n+ENSG00000205439\tKRTAP12-3\n+ENSG00000221864\tKRTAP12-2\n+ENSG00000187175\tKRTAP12-1\n+ENSG00000189169\tKRTAP10-12\n+ENSG00000184787\tUBE2G2\n+ENSG00000236519\tAL773604.8\n+ENSG00000184900\tSUMO3\n+ENSG00000183255\tPTTG1IP\n+ENSG00000160255\tITGB2\n+ENSG00000227039\tITGB2-AS1\n+ENSG00000183250\tC21orf67\n+ENSG00000272825\tLL21NC02-1C16.2\n+ENSG00000160256\tFAM207A\n+ENSG00000234880\tLINC00163\n+ENSG00000261706\tAP001505.9\n+ENSG00000224930\tLINC00162\n+ENSG00000268856\tAP001579.1\n+ENSG00000197381\tADARB1\n+ENSG00000268805\tPRED57\n+ENSG00000267857\tPRED58\n+ENSG00000182586\tLINC00334\n+ENSG00000186866\tPOFUT2\n+ENSG00000223768\tLINC00205\n+ENSG00000184274\tLINC00315\n+ENSG00000229382\tBX322557.13\n+ENSG00000237664\tLINC00316\n+ENSG00000228355\tBX322559.3\n+ENSG00000182871\tCOL18A1\n+ENSG00000224574\tCOL18A1-AS2\n+ENSG00000183535\tCOL18A1-AS1\n+ENSG00000173638\tSLC19A1\n+ENSG00000233922\tAL133493.2\n+ENSG00000183570\tPCBP3\n+ENSG00000267883\tPRED60\n+ENSG00000205424\tAL592528.1\n+ENSG00000268040\tPRED62\n+ENSG00000142156\tCOL6A1\n+ENSG00000224413\tAP001476.2\n+ENSG00000228235\tAP001476.4\n+ENSG00000226115\tAP001476.3\n+ENSG00000227438\tAP001471.1\n+ENSG00000142173\tCOL6A2\n+ENSG00000160282\tFTCD\n+ENSG00000237338\tFTCD-AS1\n+ENSG00000160284\tSPATC1L\n+ENSG00000228404\tAP001468.58\n+ENSG00000160285\tLSS\n+ENSG00000235878\tAP001468.1\n+ENSG00000223901\tAP001469.5\n+ENSG00000215424\tMCM3AP-AS1\n+ENSG00000160294\tMCM3AP\n+ENSG00000228137\tAP001469.7\n+ENSG00000239415\tAP001469.9\n+ENSG00000182362\tYBEY\n+ENSG00000160298\tC21orf58\n+ENSG00000160299\tPCNT\n+ENSG00000160305\tDIP2A\n+ENSG00000160307\tS100B\n+ENSG00000160310\tPRMT2\n+ENSG00000198888\tMT-ND1\n+ENSG00000198763\tMT-ND2\n+ENSG00000198804\tMT-CO1\n+ENSG00000198712\tMT-CO2\n+ENSG00000228253\tMT-ATP8\n+ENSG00000198899\tMT-ATP6\n+ENSG00000198938\tMT-CO3\n+ENSG00000198840\tMT-ND3\n+ENSG00000212907\tMT-ND4L\n+ENSG00000198886\tMT-ND4\n+ENSG00000198786\tMT-ND5\n+ENSG00000198695\tMT-ND6\n+ENSG00000198727\tMT-CYB\n+ENSG00000215642\tAL360154.1\n+ENSG00000234295\tAC109135.1\n+ENSG00000215750\tAC145212.1\n+ENSG00000215689\tMGC39584\n+ENSG00000229510\tAC018692.2\n+ENSG00000220903\tFRG2C\n+ENSG00000233094\tAL592170.1\n+ENSG00000212857\tAL356585.1\n+ENSG00000215781\tAC011043.1\n+ENSG00000218497\tZNF84\n+ENSG00000236575\tZNF26\n+ENSG00000229631\tAL603926.1\n+ENSG00000220023\tAL592183.1\n+ENSG00000212884\tAC011841.1\n+ENSG00000268851\tAL162851.1\n+ENSG00000269725\tBX072566.2\n+ENSG00000237375\tBX072566.1\n+ENSG00000215615\tAL354822.1\n+ENSG00000215764\tKIR2DL2\n+ENSG00000217792\tKIR3DL2\n+ENSG00000268276\tAL590523.1\n+ENSG00000148828\tCT476828.1\n+ENSG00000215700\tPNRC2\n+ENSG00000215699\tSRSF10\n+ENSG00000215635\tAC145205.1\n+ENSG00000268590\tBAGE5\n+ENSG00000251180\tCU459201.1\n+ENSG00000215616\tAC002321.2\n+ENSG00000215611\tAC002321.1\n' |
| b |
| diff -r 000000000000 -r aab4d3a52ee3 test-data/pbmc3k.rds |
| b |
| Binary file test-data/pbmc3k.rds has changed |
| b |
| diff -r 000000000000 -r aab4d3a52ee3 test-data/pbmc3k_filtered_gene_bc_matrices.tar.gz |
| b |
| Binary file test-data/pbmc3k_filtered_gene_bc_matrices.tar.gz has changed |
| b |
| diff -r 000000000000 -r aab4d3a52ee3 test-data/pbmc3k_sc3.rds |
| b |
| Binary file test-data/pbmc3k_sc3.rds has changed |
| b |
| diff -r 000000000000 -r aab4d3a52ee3 test-data/scater_log.rds |
| b |
| Binary file test-data/scater_log.rds has changed |
| b |
| diff -r 000000000000 -r aab4d3a52ee3 test-data/test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test Wed Apr 03 11:25:01 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ + |