Release 2
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:
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"]}]}}