New version with docker, LOOM, HCA binding and more.
| Tool | Version |
|---|---|
| java_stats | 1.0 |
| sclvm | 0.99.3 |
| gpy | 1.5.6 |
| limix | 0.8.0.dev0 |
| h5py | 2.10.0 |
| scikits_learn | 0.21.3 |
| numpy | 1.17.2 |
| scipy | 1.3.1 |
| java | 1.8.0_111 |
| python | 2.7.5 |
| combat | 3.30.1 |
| stats | 3.5.0 |
| sc3 | 1.10.1 |
| mds | 7.3-50 |
| pam | 2.0.7-1 |
| zifa | 0.1 |
| rtsne | 0.15 |
| pagoda_scde | 2.10.1 |
| limma_voom | 3.38.3 |
| edger | 3.24.3 |
| deseq2 | 1.22.2 |
| scan_upc | 2.18.0 |
| datatable | 1.12.0 |
| go_db | 2017-Jun |
| kegg_db | 2016-Nov |
| gsea_db | 2016-Nov |
| gene_atlas_db | 2016-Nov |
| ensembl_vertebrate | 97 |
| ensembl_genomes | 58 |
{
"name": "fabdavid/asap_run",
"tag": "v4",
"version": 4,
"call": "docker run #host_option --name #container_name --network=asap2_asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap2:/data/asap2 #image_name -c"
}
{
"r": "3.5.0",
"hdf5r": "1.0.1",
"xvector": "0.22.0",
"sc3": "1.10.1",
"scater": "1.10.1",
"limma_voom": "3.38.3",
"deseq2": "1.22.2",
"combat": "3.30.1",
"genefilter": "1.64.0",
"m3drop": "3.10.3",
"rhdf5": "2.31.3",
"seurat": "3.1.3",
"future.apply": "1.3.0",
"plotly": "4.8.0",
"statmod": "1.4.30",
"devtools": "2.0.1",
"datatable": "1.12.0",
"jsonlite": "1.6",
"rtsne": "0.15",
"r6": "2.4.0",
"reticulate": "1.11.1",
"python": "2.7.16",
"h5py": "2.9.0",
"leidenalg": "0.7.0",
"numba": "0.42.0",
"numpy": "1.16.2",
"scikit_learn": "0.20.3",
"scipy": "1.2.1",
"umap_learn": "0.3.7",
"java": "11.0.2"
}
fabdavid/asap_run (v4)
{"tool_versions":{"java_stats":"1.0","sclvm":"0.99.3","gpy":"1.5.6","limix":"0.8.0.dev0","h5py":"2.10.0","scikits_learn":"0.21.3","numpy":"1.17.2","scipy":"1.3.1","java":"1.8.0_111","python":"2.7.5","combat":"3.30.1","stats":"3.5.0","sc3":"1.10.1","mds":"7.3-50","pam":"2.0.7-1","zifa":"0.1","rtsne":"0.15","pagoda_scde":"2.10.1","limma_voom":"3.38.3","edger":"3.24.3","deseq2":"1.22.2","scan_upc":"2.18.0","datatable":"1.12.0","go_db":"2017-Jun","kegg_db":"2016-Nov","gsea_db":"2016-Nov","gene_atlas_db":"2016-Nov","ensembl_vertebrate":"97","ensembl_genomes":"58"},"asap_data_db_version":4,"docker_images":{"asap_run":{"name":"fabdavid/asap_run","tag":"v4","version":4,"call":"docker run #host_option --name #container_name --network=asap2_asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap2:/data/asap2 #image_name -c"}},"time_call":"time -o '#output_dir/exec_run_details.log' -f 'U=%U,S=%S,E=%E,P=%P,X=%X,D=%D,M=%M,K=%K,t=%t,I=%I,O=%O,F=%F,R=%R,W=%W' ","exec_stdout":"#output_dir/exec.out","exec_stderr":"#output_dir/exec.err","hosts":{"localhost":{"nb_cores":80}},"asap_run_java":"ASAP-2.0.jar","types":{"dataset":{"description":"Matrix of values of any dimension and containing any type of data"},"int_matrix":{"description":"Count matrix (the matrix must contain only integer values)"},"num_matrix":{"description":"Numeric matrix (the matrix can contain integer or floating point values)"},"with_mdata_ercc":{"description":"Metadata for ERCC must exist."},"discrete_mdata":{"description":"Categorical metadata"},"numeric_mdata":{"description":"Numerical metadata"},"string_mdata":{"description":"Text metadata"},"col_mdata":{"description":"Cell metadata"},"row_mdata":{"description":"Gene metadata"},"mdata":{"description":"Metadata"}},"dashboards":{"std_runs":{"icon_class":"fa fa-bars"},"dim_reduction":{"icon_class":"scatter_plot-icon"}},"compliance":{"1":[{"name":"scFAIR","version":"7.1.0","source_schema_name":"scFAIR schema","description":"scFAIR validates single-cell transcriptomics datasets against the scFAIR cell metadata schema","source_url":"https://github.com/scFAIR/scFAIR/blob/main/schema/7.1.0/README.md","url":"https://sc-fair.org","compliant_icon":"scfair_badge_compliant.svg","not_compliant_icon":"scfair_badge_noncompliant.svg","if_compliant":["allow_public"]}]},"asap_data_db_name":"asap_data_v4"}