Release 7
Release 7
November 08, 2023
Activated
Description
Updated docker. New single-cell specific pipeline using Seurat.
Compliance Schemas
sc
scFAIR v7.1.0
(scFAIR schema v7.1.0)
Schema reference
Website
Loom Path Translation
Required for publishing
scFAIR validates single-cell transcriptomics datasets against the scFAIR cell metadata schema
Badges:
Tool Versions
| Tool | Version |
|---|---|
| java_stats | 1.0 |
| java | 11.0.6 |
| go_db | 2020-Jan |
| ensembl_vertebrate | 104 |
| ensembl_genomes | 58 |
| hcao | |
| fbbt |
Docker Images
Raw metadata
{
"name": "fabdavid/asap_run",
"tag": "v6",
"version": 6,
"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/asap:/data/asap -v /srv/asap_run/srv:/srv #image_name -c"
}
DockerImage.tools_json
{
"r": "4.3.1",
"hdf5r": "1.3.8",
"scran": "1.28.2",
"xvector": "0.40.0",
"sc3": "1.28.3",
"scater": "1.28.0",
"cluster": "2.1.4",
"limma_voom": "3.56.2",
"deseq2": "1.40.2",
"combat": "3.48.0",
"genefilter": "1.82.1",
"m3drop": "3.10.6",
"rhdf5": "2.45.2",
"seurat": "4.4.0",
"future.apply": "1.11.0",
"plotly": "4.10.2",
"statmod": "1.5.0",
"devtools": "2.4.5",
"datatable": "1.14.8",
"jsonlite": "1.8.7",
"rtsne": "0.16",
"bit64": "4.0.5",
"r6": "2.5.1",
"sanon": "1.6",
"reticulate": "1.34.0",
"edger": "3.42.4",
"python3": "3.11.6",
"h5py": "3.9.0",
"leidenalg": "0.10.1",
"loompy": "3.0.7",
"matplotlib": "3.6.3",
"numba": "0.57.1",
"numpy": "1.24.2",
"pandas": "1.5.3",
"scikit_learn": "1.3.1",
"scipy": "1.10.1",
"umap_learn": "0.5.4",
"java": "17.0.9"
}
fabdavid/asap_run (v6)
Java
Python
R
Raw environment JSON
{"tool_versions":{"java_stats":"1.0","java":"11.0.6","go_db":"2020-Jan","ensembl_vertebrate":"104","ensembl_genomes":"58","hcao":null,"fbbt":null},"asap_data_db_version":6,"docker_images":{"asap_run":{"name":"fabdavid/asap_run","tag":"v6","version":6,"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/asap:/data/asap -v /srv/asap_run/srv:/srv #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_v6"}