# SDAS Manual ## SDAS Manual - [Stereo Data Analysis Solution (SDAS) User Manual](https://mysite.gitbook.io/sdas_manual_eng/readme.md): Version: SDAS 1.0.0 - [Software Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/01_sdas_intro.md) - [Installation Guide](https://mysite.gitbook.io/sdas_manual_eng/readme/02_install.md) - [Quick Start](https://mysite.gitbook.io/sdas_manual_eng/readme/03_quickstart.md) - [Instructions for Each Functional Module](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual.md) - [SDAS Input Data Format Description](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/sdas_input.md) - [Performance Test Environment and Data Description](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/sdas_test_data.md) - [Data Processing](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/dataprocess.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/dataprocess/01_intro.md) - [Input File Example](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/dataprocess/02_input.md) - [Command Description](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/dataprocess/03_function.md) - [Cell Type Annotation](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation/01_intro.md) - [h5ad Data Format Description](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation/02_input.md) - [cell2location Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation/03_cell2location.md) - [Build Single-cell Reference Data](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation/03_cell2location/01_ref.md) - [Cell Annotation](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation/03_cell2location/02_anno.md) - [RCTD Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation/04_rctd.md) - [Tangram Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation/05_tangram.md) - [SCimilarity Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation/06_scimilarity.md) - [Build Single-cell Reference Data (Optional)](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation/06_scimilarity/01_ref.md) - [Cell Annotation](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation/06_scimilarity/02_anno.md) - [SPOTlight Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation/07_spotlight.md) - [Performance Test](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_annotation/08_performence.md) - [Spatial Domain Identification](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/spatial_domain.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/spatial_domain/01_intro.md) - [h5ad Data Format Description](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/spatial_domain/02_input.md) - [graphST Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/spatial_domain/03_graphst.md) - [Performance Test](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/spatial_domain/xing-neng-ce-shi.md) - [Cellular Neighborhood Analysis](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_neighborhood.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_neighborhood/01_intro.md) - [Single Cell Type Mode](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_neighborhood/02_singlecell.md) - [Cell Type Score Mode](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_neighborhood/03_multicell.md) - [Performance Test](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cell_neighborhood/04_perfermence.md) - [CNV Analysis](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cnv.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cnv/01_intro.md) - [Input File Example](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cnv/02_input.md) - [InferCNV Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cnv/03_infercnv.md) - [Performance Test](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cnv/04_performence.md) - [Spatial Gene Co-expression](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/coexpress.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/coexpress/01_intro.md) - [Input File Example](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/coexpress/02_input.md) - [hdWGCNA Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/coexpress/03_hdwgcna.md) - [Hotspot Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/coexpress/04_hotspot.md) - [NeST Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/coexpress/05_nest.md) - [Performance Test](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/coexpress/06_performence.md) - [Differential Gene Analysis](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/deg.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/deg/01_intro.md) - [Input File Example](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/deg/02_input.md) - [Single-cell/pseudobulk Differential Analysis](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/deg/03_deg.md) - [Performance Test](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/deg/04_performence.md) - [Gene Set Enrichment Analysis](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/geneset_enrichment.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/geneset_enrichment/01_intro.md) - [Input File Example](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/geneset_enrichment/02_input.md) - [GSEA Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/geneset_enrichment/03_gsea.md) - [GSVA Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/geneset_enrichment/04_gsva.md) - [Enrichr Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/geneset_enrichment/05_enrich.md) - [Prerank Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/geneset_enrichment/06_prerank.md) - [Performance Test](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/geneset_enrichment/07_performence.md) - [Protein Interaction Network Analysis](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/ppi.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/ppi/01_intro.md) - [Input File Example](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/ppi/02_input.md) - [GN/MCL/Kmeans Clustering](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/ppi/03_function.md) - [Cell Communication Analysis](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cci.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cci/01_intro.md) - [Input File Example](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cci/02_input.md) - [cellchat Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cci/03_cellchat.md) - [cellphonedb Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cci/04_cellphonedb.md) - [Performance Test](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/cci/05_performence.md) - [Trajectory Analysis](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/trajectory.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/trajectory/01_intro.md) - [Input File Example](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/trajectory/02_input.md) - [monocle3 Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/trajectory/03_monocle3.md) - [Performance Test](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/trajectory/04_performence.md) - [Transcription Factor Analysis](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/tf.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/tf/01_intro.md) - [Input File Example](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/tf/02_input.md) - [pyscenic Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/tf/03_pyscenic.md) - [Performance Test](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/tf/04_performence.md) - [Cell-type Spatial Relationship Analysis](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/spatial_relate.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/spatial_relate/01_intro.md) - [Input File Example](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/spatial_relate/02_input.md) - [Squidpy Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/spatial_relate/03_squidpy.md) - [CRAWDAD Algorithm](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/spatial_relate/04_crawdad.md) - [Performance Test](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/spatial_relate/05_performence.md) - [Public Bulk Database Validation](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/bulk_validate.md) - [Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/bulk_validate/00_intro.md) - [Immune Infiltration Analysis Module](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/bulk_validate/01_immune.md) - [Gene Set Scoring Module](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/bulk_validate/02_geneset.md) - [Survival Analysis Module](https://mysite.gitbook.io/sdas_manual_eng/readme/04_manual/bulk_validate/03_survival.md) - [Pipeline Example](https://mysite.gitbook.io/sdas_manual_eng/readme/05_pipline.md) - [Cluster Submission Mode​](https://mysite.gitbook.io/sdas_manual_eng/readme/05_pipline/02_qsub.md) - [​​Standalone Mode​](https://mysite.gitbook.io/sdas_manual_eng/readme/05_pipline/01_single.md) - [Release Notes](https://mysite.gitbook.io/sdas_manual_eng/readme/06_version.md) - [Support](https://mysite.gitbook.io/sdas_manual_eng/readme/07_support.md) - [Frequently Asked Questions](https://mysite.gitbook.io/sdas_manual_eng/readme/07_support/faq.md) - [SDAS Log and Exit Code Specification](https://mysite.gitbook.io/sdas_manual_eng/readme/07_support/log.md) - [SAW aggr (alpha ver.) Pipeline Introduction](https://mysite.gitbook.io/sdas_manual_eng/readme/07_support/saw_aggr.md) - [Reference and Github](https://mysite.gitbook.io/sdas_manual_eng/readme/07_support/reference.md)