ASAP Releases

Release notes and changelog for ASAP versions.

Release 8 December 29, 2024 Beta

Description

Updated docker. Updated database. New input format: Seurat objects as .rds files.

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
java 11.0.6
go_db 2024-11-03
ensembl_vertebrate 113
ensembl_genomes 60
hcao
fbbt
panglaodb 2020

Docker Images

Raw metadata
{
  "name": "fabdavid/asap_run",
  "tag": "v8",
  "version": 8,
  "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 --env-file .env_asap_run #image_name -c"
}
DockerImage.tools_json
{
  "r": "4.4.3",
  "hdf5r": "1.3.12",
  "scran": "1.34.0",
  "xvector": "0.46.0",
  "sc3": "1.34.0",
  "scater": "1.34.1",
  "cluster": "2.1.8.1",
  "limma_voom": "3.62.2",
  "deseq2": "1.46.0",
  "combat": "3.54.0",
  "genefilter": "1.88.0",
  "m3drop": "3.10.6",
  "rhdf5": "2.51.2",
  "seurat": "5.2.1",
  "future.apply": "1.11.3",
  "plotly": "4.10.4",
  "statmod": "1.5.0",
  "devtools": "2.4.5",
  "datatable": "1.17.0",
  "jsonlite": "1.9.1",
  "rtsne": "0.17",
  "r6": "2.6.1",
  "sanon": "1.6",
  "reticulate": "1.41.0.1",
  "edger": "4.4.2",
  "python3": "3.12.7",
  "h5py": "3.12.1",
  "leidenalg": "0.10.2",
  "loompy": "3.0.7",
  "matplotlib": "3.10.0",
  "numba": "0.60.0",
  "numpy": "2.0.2",
  "pandas": "2.2.3",
  "scikit_learn": "1.6.0",
  "scipy": "1.15.0",
  "umap_learn": "0.5.7",
  "java": "17.0.14"
}
Raw environment JSON
{"tool_versions":{"java_stats":"1.0","java":"11.0.6","go_db":"2024-11-03","ensembl_vertebrate":"113","ensembl_genomes":"60","hcao":null,"fbbt":null,"panglaodb":"2020"},"asap_data_db_version":8,"docker_images":{"asap_run":{"name":"fabdavid/asap_run","tag":"v8","version":8,"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 --env-file .env_asap_run #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_v8"}
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: scfair_badge_compliant.svg scfair_badge_noncompliant.svg

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"
}
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"}
Release 6 April 12, 2022 Activated

Description

Ensembl update.

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
java 11.0.6
go_db 2020-Jan
ensembl_vertebrate 104
ensembl_genomes 58
hcao 2020-06-01
fbbt 2021-12-09

Docker Images

Raw metadata
{
  "name": "fabdavid/asap_run",
  "tag": "v5",
  "version": 5,
  "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": "3.6.2",
  "hdf5r": "1.3.4",
  "scran": "1.14.6",
  "xvector": "0.26.0",
  "sc3": "1.14.0",
  "scater": "1.14.6",
  "cluster": "2.1.0",
  "limma_voom": "3.42.2",
  "deseq2": "1.26.0",
  "combat": "3.34.0",
  "genefilter": "1.68.0",
  "m3drop": "3.10.4",
  "rhdf5": "2.31.11",
  "seurat": "3.1.5",
  "future.apply": "1.5.0",
  "plotly": "4.9.2.1",
  "statmod": "1.4.34",
  "devtools": "2.3.0",
  "datatable": "1.12.8",
  "jsonlite": "1.6.1",
  "rtsne": "0.15",
  "r6": "2.4.1",
  "sanon": "1.6",
  "reticulate": "1.15",
  "edger": "3.28.1",
  "python3": "3.7.6",
  "h5py": "3.1.0",
  "leidenalg": "0.8.7",
  "loompy": "3.0.6",
  "louvain": "0.7.0",
  "matplotlib": "3.3.2",
  "numba": "0.53.1",
  "numpy": "1.20.3",
  "pandas": "1.2.4",
  "scikit_learn": "0.24.2",
  "scipy": "1.6.3",
  "umap_learn": "0.5.1",
  "java": "11.0.6"
}
Raw environment JSON
{"tool_versions":{"java_stats":"1.0","java":"11.0.6","go_db":"2020-Jan","ensembl_vertebrate":"104","ensembl_genomes":"58","hcao":"2020-06-01","fbbt":"2021-12-09"},"asap_data_db_version":6,"docker_images":{"asap_run":{"name":"fabdavid/asap_run","tag":"v5","version":5,"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"}
Release 5 February 12, 2020 Activated

Description

Optimized asap_run docker, migration of v.2.7 python scripts to v.3.0. Updated Ensembl data in asap_data database.

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
h5py 2.10.0
scikits_learn 0.22.1
numpy 1.18.1
scipy 1.4.1
java 11.0.6
python 3.7.6
stats 3.6.0
sc3 1.14.0
cluster 2.1.0
rtsne 0.15
limma_voom 3.42.2
deseq2 1.26.0
umap-learn 0.3.10
datatable 1.12.8
go_db 2020-Jan
ensembl_vertebrate 101
ensembl_genomes 58

Docker Images

Raw metadata
{
  "name": "fabdavid/asap_run",
  "tag": "v5",
  "version": 5,
  "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": "3.6.2",
  "hdf5r": "1.3.4",
  "scran": "1.14.6",
  "xvector": "0.26.0",
  "sc3": "1.14.0",
  "scater": "1.14.6",
  "cluster": "2.1.0",
  "limma_voom": "3.42.2",
  "deseq2": "1.26.0",
  "combat": "3.34.0",
  "genefilter": "1.68.0",
  "m3drop": "3.10.4",
  "rhdf5": "2.31.11",
  "seurat": "3.1.5",
  "future.apply": "1.5.0",
  "plotly": "4.9.2.1",
  "statmod": "1.4.34",
  "devtools": "2.3.0",
  "datatable": "1.12.8",
  "jsonlite": "1.6.1",
  "rtsne": "0.15",
  "r6": "2.4.1",
  "sanon": "1.6",
  "reticulate": "1.15",
  "edger": "3.28.1",
  "python3": "3.7.6",
  "h5py": "3.1.0",
  "leidenalg": "0.8.7",
  "loompy": "3.0.6",
  "louvain": "0.7.0",
  "matplotlib": "3.3.2",
  "numba": "0.53.1",
  "numpy": "1.20.3",
  "pandas": "1.2.4",
  "scikit_learn": "0.24.2",
  "scipy": "1.6.3",
  "umap_learn": "0.5.1",
  "java": "11.0.6"
}
Raw environment JSON
{"tool_versions":{"java_stats":"1.0","h5py":"2.10.0","scikits_learn":"0.22.1","numpy":"1.18.1","scipy":"1.4.1","java":"11.0.6","python":"3.7.6","stats":"3.6.0","sc3":"1.14.0","cluster":"2.1.0","rtsne":"0.15","limma_voom":"3.42.2","deseq2":"1.26.0","umap-learn":"0.3.10","datatable":"1.12.8","go_db":"2020-Jan","ensembl_vertebrate":"101","ensembl_genomes":"58"},"asap_data_db_version":5,"docker_images":{"asap_run":{"name":"fabdavid/asap_run","tag":"v5","version":5,"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_v5"}
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/asap:/data/asap  #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/asap:/data/asap  #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"}
Release 3 April 12, 2018 Activated

Description

New version including: -New trajectory visualization (Monocle) -Project sharing -Searchable list of projects / analyses

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 2.6.0
scikits_learn 0.18.1
numpy 1.11.2
scipy 0.18.1
java 1.8.0_111
python 2.7.5
combat 3.24.4
stats 3.3.1
sc3 1.3.11
mds 7.3-45
pam 2.0.6
zifa 0.1
rtsne 0.13
pagoda_scde 2.5.0
limma_voom 3.32.2
edger 3.18.1
deseq2 1.16.1
scan_upc 2.18.0
datatable 1.10.4
go_db 2017-Jun
kegg_db 2016-Nov
gsea_db 2016-Nov
gene_atlas_db 2016-Nov
ensembl 2017-Mar
Raw environment JSON
{"tool_versions":{"java_stats":"1.0","sclvm":"0.99.3","gpy":"1.5.6","limix":"0.8.0.dev0","h5py":"2.6.0","scikits_learn":"0.18.1","numpy":"1.11.2","scipy":"0.18.1","java":"1.8.0_111","python":"2.7.5","combat":"3.24.4","stats":"3.3.1","sc3":"1.3.11","mds":"7.3-45","pam":"2.0.6","zifa":"0.1","rtsne":"0.13","pagoda_scde":"2.5.0","limma_voom":"3.32.2","edger":"3.18.1","deseq2":"1.16.1","scan_upc":"2.18.0","datatable":"1.10.4","go_db":"2017-Jun","kegg_db":"2016-Nov","gsea_db":"2016-Nov","gene_atlas_db":"2016-Nov","ensembl":"2017-Mar"},"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"]}]}}
Release 2 July 09, 2017 Activated

Description

New version including: - changing reading and writing methods to the 'data.table' package to speed up processing of big datasets - handling of 69 organisms (from all releases of Ensembl database) - addition of alternative gene names from old Ensembl releases - correction of minor bugs - update of R and Python libraries

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 2.6.0
scikits_learn 0.18.1
numpy 1.11.2
scipy 0.18.1
java 1.8.0_111
python 2.7.5
combat 3.24.4
stats 3.3.1
sc3 1.3.11
mds 7.3-45
pam 2.0.6
zifa 0.1
rtsne 0.13
pagoda_scde 2.5.0
limma_voom 3.32.2
edger 3.18.1
deseq2 1.16.1
scan_upc 2.18.0
datatable 1.10.4
go_db 2017-Jun
kegg_db 2016-Nov
gsea_db 2016-Nov
gene_atlas_db 2016-Nov
ensembl 2017-Mar
Raw environment JSON
{"tool_versions":{"java_stats":"1.0","sclvm":"0.99.3","gpy":"1.5.6","limix":"0.8.0.dev0","h5py":"2.6.0","scikits_learn":"0.18.1","numpy":"1.11.2","scipy":"0.18.1","java":"1.8.0_111","python":"2.7.5","combat":"3.24.4","stats":"3.3.1","sc3":"1.3.11","mds":"7.3-45","pam":"2.0.6","zifa":"0.1","rtsne":"0.13","pagoda_scde":"2.5.0","limma_voom":"3.32.2","edger":"3.18.1","deseq2":"1.16.1","scan_upc":"2.18.0","datatable":"1.10.4","go_db":"2017-Jun","kegg_db":"2016-Nov","gsea_db":"2016-Nov","gene_atlas_db":"2016-Nov","ensembl":"2017-Mar"},"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"]}]}}
Release 1 November 14, 2016 Activated

Description

This is the first version!

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 0.99.2
gpy 1.5.6
limix 0.8.0.dev0
h5py 2.6.0
scikits_learn 0.18.1
numpy 1.11.2
scipy 0.18.1
java 1.8.0_111
python 2.7.5
combat 3.18.0
stats 3.3.1
sc3 1.3.11
mds 7.3-45
pam 2.0.5
zifa 0.1
rtsne 0.11
pagoda_scde 1.99.4
limma_voom 3.26.9
edger 3.12.1
deseq2 1.10.1
scan_upc 2.12.1
go_db 2016-Nov
kegg_db 2016-Nov
gsea_db 2016-Nov
gene_atlas_db 2016-Nov
Raw environment JSON
{"tool_versions":{"java_stats":"1.0","sclvm":"0.99.2","gpy":"1.5.6","limix":"0.8.0.dev0","h5py":"2.6.0","scikits_learn":"0.18.1","numpy":"1.11.2","scipy":"0.18.1","java":"1.8.0_111","python":"2.7.5","combat":"3.18.0","stats":"3.3.1","sc3":"1.3.11","mds":"7.3-45","pam":"2.0.5","zifa":"0.1","rtsne":"0.11","pagoda_scde":"1.99.4","limma_voom":"3.26.9","edger":"3.12.1","deseq2":"1.10.1","scan_upc":"2.12.1","go_db":"2016-Nov","kegg_db":"2016-Nov","gsea_db":"2016-Nov","gene_atlas_db":"2016-Nov"},"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"]}]}}