Thymus ASAP129 v8

66 cells M. murinus

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Parsing Success 3 months ago

file_type: H5AD sel_name: /raw/X nber_rows: 16400 nber_cols: 66

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Owned by fabrice.david

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Summary Visualization Heatmap Annotations Analysis Data

Downloads

Input file List of Loom files (JSON)

Guided tours

Getting started Get project summary Visualize project Browse project data Create a new project Search projects

Info

Releases

Release notes & changelog

Project types

Available project types and their configurations

Cell ontologies

Ontology catalogs mirrored from legacy ASAP

Cell metadata schema

Cell metadata used by ASAP to annotate single-cell datasets

Cross-references

Identifier types and external database links

Atlases

FCA and HCA reference pages and entry points

External catalog

Candidate datasets from CELLxGENE, Bgee, EBI SC Atlas, HCA, GEO

File formats

Supported upload and export formats

API documentation

OpenAPI/Swagger reference for JSON endpoints

FAQ

Frequently asked questions about ASAP

Guest Mode

Sign In

Feedback

Discussions Citing ASAP Feature requests and issues Contact us Rate the app

Back to Projects

Input file List of Loom files (JSON)

Guided tours

Getting started Get project summary Visualize project Browse project data Create a new project Search projects

Releases

Release notes & changelog

Project types

Available project types and their configurations

Cell ontologies

Ontology catalogs mirrored from legacy ASAP

Cell metadata schema

Cell metadata used by ASAP to annotate single-cell datasets

Cross-references

Identifier types and external database links

Atlases

FCA and HCA reference pages and entry points

External catalog

Candidate datasets from CELLxGENE, Bgee, EBI SC Atlas, HCA, GEO

File formats

Supported upload and export formats

API documentation

OpenAPI/Swagger reference for JSON endpoints

FAQ

Frequently asked questions about ASAP

Discussions

Ask questions and share ideas

Citing ASAP

How to cite ASAP and who references it

Feature requests and issues

Report bugs or suggest improvements

Contact us

Reach the ASAP team by email

Rate the app

Share your experience with ASAP

Guest Mode

LOOM/H5AD

Categorical Metadata

74

Loading filter data...

MHC_C_I

1 categories

Category Best annotation Cells

nan

-

66

MHC_NC_I

1 categories

Category Best annotation Cells

nan

-

66

MHC_all_II

1 categories

Category Best annotation Cells

nan

-

66

Mimu_168

1 categories

Category Best annotation Cells

nan

-

66

Mimu_180ps

1 categories

Category Best annotation Cells

nan

-

66

Mimu_191

1 categories

Category Best annotation Cells

nan

-

66

Mimu_202

1 categories

Category Best annotation Cells

nan

-

66

Mimu_208

1 categories

Category Best annotation Cells

nan

-

66

Mimu_218

1 categories

Category Best annotation Cells

nan

-

66

Mimu_229ps

1 categories

Category Best annotation Cells

nan

-

66

Mimu_239ps

1 categories

Category Best annotation Cells

nan

-

66

Mimu_249

1 categories

Category Best annotation Cells

nan

-

66

Mimu_DMA

1 categories

Category Best annotation Cells

nan

-

66

Mimu_DMB

1 categories

Category Best annotation Cells

nan

-

66

Mimu_DPA

1 categories

Category Best annotation Cells

nan

-

66

Mimu_DPB

1 categories

Category Best annotation Cells

nan

-

66

Mimu_DQA

1 categories

Category Best annotation Cells

nan

-

66

Mimu_DQB

1 categories

Category Best annotation Cells

nan

-

66

Mimu_DRA

1 categories

Category Best annotation Cells

nan

-

66

Mimu_DRB

1 categories

Category Best annotation Cells

nan

-

66

Mimu_W03

1 categories

Category Best annotation Cells

nan

-

66

Mimu_W04

1 categories

Category Best annotation Cells

nan

-

66

age

1 categories

Category Best annotation Cells

11

-

66

assay

1 categories

Category Best annotation Cells

Smart-seq2

-

66

assay_ontology_term_id

1 categories

Category Best annotation Cells

EFO:0008931

-

66

cell_ontology_class_v1

9 categories

Category Best annotation Cells

capillary endothelial cell

-

26

macrophage

-

21

neutrophil

-

11

lymphocyte

-

3

mesothelial cell

-

1

endothelial cell of lymphatic vessel

-

1

endothelial cell of artery

-

1

fibroblast

-

1

fat cell

-

1

cell_type

9 categories

Category Best annotation Cells

capillary endothelial cell

-

26

macrophage

-

21

neutrophil

-

11

lymphocyte

-

3

mesothelial cell

-

1

endothelial cell of lymphatic vessel

-

1

endothelial cell of artery

-

1

fibroblast

-

1

adipocyte

-

1

cell_type_ontology_term_id

9 categories

Category Best annotation Cells

CL:0002144

-

26

CL:0000235

-

21

CL:0000775

-

11

CL:0000542

-

3

CL:0000077

-

1

CL:0002138

-

1

CL:1000413

-

1

CL:0000057

-

1

CL:0000136

-

1

compartment_v1

4 categories

Category Best annotation Cells

myeloid

-

32

endothelial

-

28

stromal

-

3

lymphoid

-

3

dendrogram_annotation_number

9 categories

Category Best annotation Cells

86

-

26

184

-

21

175

-

11

H6

-

3

134

-

1

M4

-

1

77

-

1

111

-

1

132

-

1

development_stage

1 categories

Category Best annotation Cells

post-juvenile adult stage

-

66

development_stage_ontology_term_id

1 categories

Category Best annotation Cells

UBERON:0000113

-

66

disease

1 categories

Category Best annotation Cells

normal

-

66

disease_ontology_term_id

1 categories

Category Best annotation Cells

PATO:0000461

-

66

donor_id

1 categories

Category Best annotation Cells

L4

-

66

free_annotation_v1

9 categories

Category Best annotation Cells

capillary cell (FABP5+ RBP7+)

-

26

macrophage

-

21

neutrophil

-

11

natural killer cell_T cell

-

3

mesothelial cell

-

1

lymphatic cell

-

1

artery cell

-

1

fibroblast

-

1

adipocyte (UCP1hi)

-

1

general_tissue

1 categories

Category Best annotation Cells

Thymus

-

66

is_primary_data

1 categories

Category Best annotation Cells

False

-

66

low_quality

1 categories

Category Best annotation Cells

unassigned

-

66

mix_hybrid

3 categories

Category Best annotation Cells

unassigned

-

62

hybrid

-

3

mix

-

1

nMHC_C_I

1 categories

Category Best annotation Cells

nan

-

66

nMHC_NC_I

1 categories

Category Best annotation Cells

nan

-

66

nMHC_all_II

1 categories

Category Best annotation Cells

nan

-

66

nMimu_168

1 categories

Category Best annotation Cells

nan

-

66

nMimu_180ps

1 categories

Category Best annotation Cells

nan

-

66

nMimu_191

1 categories

Category Best annotation Cells

nan

-

66

nMimu_202

1 categories

Category Best annotation Cells

nan

-

66

nMimu_208

1 categories

Category Best annotation Cells

nan

-

66

nMimu_218

1 categories

Category Best annotation Cells

nan

-

66

nMimu_229ps

1 categories

Category Best annotation Cells

nan

-

66

nMimu_239ps

1 categories

Category Best annotation Cells

nan

-

66

nMimu_249

1 categories

Category Best annotation Cells

nan

-

66

nMimu_DMA

1 categories

Category Best annotation Cells

nan

-

66

nMimu_DMB

1 categories

Category Best annotation Cells

nan

-

66

nMimu_DPA

1 categories

Category Best annotation Cells

nan

-

66

nMimu_DPB

1 categories

Category Best annotation Cells

nan

-

66

nMimu_DQA

1 categories

Category Best annotation Cells

nan

-

66

nMimu_DQB

1 categories

Category Best annotation Cells

nan

-

66

nMimu_DRA

1 categories

Category Best annotation Cells

nan

-

66

nMimu_DRB

1 categories

Category Best annotation Cells

nan

-

66

nMimu_W03

1 categories

Category Best annotation Cells

nan

-

66

nMimu_W04

1 categories

Category Best annotation Cells

nan

-

66

possibly_contaminated_barcode_10x

1 categories

Category Best annotation Cells

unassigned

-

66

self_reported_ethnicity

1 categories

Category Best annotation Cells

na

-

66

self_reported_ethnicity_ontology_term_id

1 categories

Category Best annotation Cells

na

-

66

sex

1 categories

Category Best annotation Cells

male

-

66

sex_ontology_term_id

1 categories

Category Best annotation Cells

PATO:0000384

-

66

subtissue

1 categories

Category Best annotation Cells

unassigned

-

66

suspension_type

1 categories

Category Best annotation Cells

cell

-

66

tissue

1 categories

Category Best annotation Cells

thymus

-

66

tissue_ontology_term_id

1 categories

Category Best annotation Cells

UBERON:0002370

-

66

tissue_order

1 categories

Category Best annotation Cells

14

-

66

tissue_system

1 categories

Category Best annotation Cells

circulatory

-

66

tissue_type

1 categories

Category Best annotation Cells

tissue

-

66

CellID

observation_joinid

Continuous Metadata

8

_Depth

All cells have the same value:

Selected: 0 cells

Ignore 0s x-axis

_Detected_Genes

All cells have the same value:

Selected: 0 cells

Ignore 0s x-axis

_Mitochondrial_Content

All cells have the same value:

Selected: 0 cells

Ignore 0s x-axis

_Protein_Coding_Content

All cells have the same value:

Selected: 0 cells

Ignore 0s x-axis

_Ribosomal_Content

All cells have the same value:

Selected: 0 cells

Ignore 0s x-axis

_StableID

All cells have the same value:

Selected: 0 cells

Ignore 0s x-axis

nCount_RNA

All cells have the same value:

Selected: 0 cells

Ignore 0s x-axis

nFeature_RNA

All cells have the same value:

Selected: 0 cells

Ignore 0s x-axis

Parsing P... > X_pca [1,2] 66 cells x 16'400 genes

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General

Main plot

Custom plot

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UMAP Plot

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Click to pick a cell, click and drag to move a label, scroll to zoom

66 / 66

Genes

-

Values from /layers/X

/matrix

/layers/X /layers/X

Cell sets Gene sets

0 visible cells view limited

selection

complement

Sort cell sets

Sort by Order

Filter cell sets

No cell sets yet

GO Biological Processes

15515 gene sets

GO Cellular Components

2066 gene sets

GO Molecular Functions

5006 gene sets

KEGG pathways

180 gene sets

No gene set collections yet

No gene sets found

Plot Settings

General settings

Dot Size

1.0

Discrete color palette

Category order

Numerical order

Histograms Gene expression only Scale Ignore 0 values

Main plot settings

Show Grid

Show Scale

Label settings

Show Category Labels

Label boxes

Label text size

Truncate long labels

Keep moved labels fixed

Reset label placement

Custom plot settings

X-axis scale

Y-axis scale

Custom plot settings are available when a custom plot is active.

Apply palette change

Some category colors were set manually. Choose how to apply the new palette.

Save checkpoint

New checkpoint

Name

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Checkpoint

You can update your own uncommented checkpoints and uncommented checkpoints created by someone else. Checkpoints that already have comments stay unchanged.

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Checkpoint history

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Existing checkpoint

Select checkpoint

Compose selection

Preview embedding

Fan-out metadata

Preview category

Operand A

Operation

Operand B

Composition steps

Batch metadata name

Auto shape: fanout.with.operands.batch_compose. Multi-step uses nested parentheses, e.g. ((region_AND_x)_OR_y). Clear to regenerate.

Metadata name already exists

Rename previous to (must end with .batch_compose)

Differential expression

Embedding for preview

Comparison

Selected vs complementary Group vs group

Reference group

Compared group

DE compares the reference group against all other cells (complementary).

Method

FDR <= |FC| >= Refreshing...

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Cell Set details

Steps lineage

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Range Selection

Metadata:

Range:

Value Range:

to

0 100

Distribution:

Customize Color Gradient

Click on the gradient bar to add control points. Drag control points to change their position, or click them to edit their color and value.

Value scale

Maps data values to the gradient.

NaN / missing color

Used for NaN and other values that cannot be mapped onto the gradient.

Gradient Preview - Click to add control points

Value distribution

Click the gradient to add a control point. Hover the gradient or histogram to see value, color, and counts.

Edit Control Point

Data Value

Color

Custom plot

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Import metadata

Type

Delimiter

Format

Input method

A simple list of identifiers (cells or genes), one per delimiter. A tab-separated table with identifiers in the first column and metadata values in the following columns. The first row must contain column headers. Global metadata stored at the file level. The content can be free text or JSON.

With column header

Name

Content

File

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.txt, .csv, .tsv

Copy one metadata column from another project you can read, with the same cell-set identity as this project (Modes A and B discovery).

By cell set By source project key

Cell set

Source project key

Preview

Annotations

Gene details

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