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SPADE specifications


Unique identifier OMICS_05639
Alternative name Spanning tree Progression of Density normalized Events
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available

Additional information

Publications for Spanning tree Progression of Density normalized Events

SPADE citations


DRUG NEM: Optimizing drug combinations using single cell perturbation response to account for intratumoral heterogeneity

Proc Natl Acad Sci U S A
PMCID: 5939057
PMID: 29654148
DOI: 10.1073/pnas.1711365115

[…] orange (Das), and green (Tof) for UPN1 and UPN7, respectively.To account for intratumor heterogeneity, we initiated DRUG-NEM with a minimum of five subpopulations based on exploratory clustering with SPADE () (Fig. S5) and then applied CCAST to identify and match seven cell subpopulations across the three inhibitors and basal (pretreatment) conditions for each patient sample (). The CCAST-derived […]


Molecular transitions in early progenitors during human cord blood hematopoiesis

Mol Syst Biol
PMCID: 5852373
PMID: 29545397
DOI: 10.15252/msb.20178041

[…] span all the vertices, in this case micro‐clusters, of a connected graph with the minimum sum of edge lengths. It has been previously applied to several trajectory‐finding methods such as Monocle and SPADE (Qiu et al, ; Trapnell et al, ).Prior to MST construction, we pre‐processed our micro‐cluster dataset using the same variable gene selection, normalization, and cell cycle regression strategy as […]


miR200 regulated CXCL12β promotes fibroblast heterogeneity and immunosuppression in ovarian cancers

Nat Commun
PMCID: 5849633
PMID: 29535360
DOI: 10.1038/s41467-018-03348-z

[…] D31− cells were next examined using the six CAF markers including CD29, FAP, SMA, FSP1, PDGFRβ, and Caveolin. Sorting of CAF subsets after surface staining was performed on FACSARIA (BD Biosciences). SPADE algorithm was performed using Cytobank (Cytobank Inc., Mountain View, CA, USA). SPADE clustering was performed using 300 nodes to generate unified trees based on the expression of the six CAF ma […]


Distinct predictive biomarker candidates for response to anti CTLA 4 and anti PD 1 immunotherapy in melanoma patients

PMCID: 5840795
PMID: 29510697
DOI: 10.1186/s40425-018-0328-8

[…] iles were assessed separately. Files were grouped into responders and non-responders. Seven surface lineage markers, CD19, CD4, CD8, CD3, CD33, CD14, and CD56 were used as clustering channels. Unlike SPADE and some other clustering algorithms, Citrus presents events redundantly in the tree, with each parent cluster containing all the events in its children, and children of children. This starts wi […]


Importance of immune monitoring approaches and the use of immune checkpoints for the treatment of diffuse intrinsic pontine glioma: From bench to clinic and vice versa (Review)

PMCID: 5843403
PMID: 29484440
DOI: 10.3892/ijo.2018.4283

[…] s being performed with several technologies and different software. Examples of these technologies are flow cytometry and CyTOF; the analyses are made using specific software including FlowJo, viSNE, SPADE, Scaffold and CITRUS.In conclusion, substantial improvement has been made in the development of cancer immunotherapy. Immune monitoring studies have identified certain biomarkers which are able […]


Prime and Boost Vaccination Elicit a Distinct Innate Myeloid Cell Immune Response

Sci Rep
PMCID: 5814452
PMID: 29449630
DOI: 10.1038/s41598-018-21222-2

[…] Cell populations were identified using the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm. Briefly, a random pre-downsampling was used to select 60,000 cells from each sample (60,000 corresponded to the number of cells contained in the smallest sample -Table ). Then the SP […]


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SPADE institution(s)
Department of Radiology, Stanford University, Stanford, CA, USA

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