Release 4

Release 4 February 01, 2019 Activated

Description

New version with docker, LOOM, HCA binding and more.

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: scfair_badge_compliant.svg scfair_badge_noncompliant.svg

Tool Versions

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

Docker Images

Raw metadata
{
  "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"
}
DockerImage.tools_json
{
  "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"
}
Raw environment JSON
{"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"}