Tirosh_2016_T_cells ASAP21 v5

2,068 cells H. sapiens

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Success Runs (12)

Gene Enrichment #1 - Fisher's Exact Test 8 months ago

input_de: Differential expr... fdr_cutoff: 0.05 fc_cutoff: 1 gene_set_id: 52 adj_method: fdr min: 15 max: 500

Differential expression #2 - Wilcoxon [Seurat] 8 months ago

input_matrix: Normalization #1 ... groups: 1 datasets all_against_compl: false group_pairs: [] group_ref: 1 group_comp: 2 min_pct: 0.25 min_diff_pct: fc_threshold: 0.2 max_cells_per_ident:

Differential expression #1 - Wilcoxon [Seurat] 8 months ago

input_matrix: Normalization #1 ... groups: 1 datasets all_against_compl: false group_pairs: [] group_ref: 1 group_comp: 2 min_pct: 0.1 min_diff_pct: fc_threshold: 1.3 max_cells_per_ident:

Clustering #3 - K-Means 8 months ago

input_matrix: Scaling #1 /layer... nb_clust: 2:10 algorithm: Hartigan-Wong

Clustering #2 - Seurat 8 months ago

input_matrix: Scaling #1 /layer... k: 20 resolution: 1 algorithm: louvain graph_type: snn

Dimension reduction #1 - UMAP 8 months ago

input_matrix: Scaling #1 /layer... nber_dims: 2 min_dist: 0.1 n_neighbors: 30 metric: correlation

Clustering #1 - Seurat 8 months ago

input_matrix: Scaling #1 /layer... k: 20 resolution: 0.8 algorithm: louvain graph_type: snn

Scaling #1 - Seurat [ASAP impl.] 8 months ago

input_matrix: Normalization #1 ... do_scale: true do_center: true scale_max: 10

Normalization #1 - Seurat [ASAP impl.] 8 months ago

input_matrix: Gene filtering #1... scale_factor: 10000

Gene filtering #1 - Basic 8 months ago

input_matrix: Cell filtering #1...

Cell filtering #1 - QC plots 8 months ago

manual_selection: discarded_metadata_json: {} depth: 4744 detected_genes: 1370 mito_content: 0 protein_coding_content: 80 ribo_content: 0 manually_discarded_cols: 965e724ec09... nber_manually_discarded_cols: 0 discarded_cols: 289c5618f00... input_matrix: Parsing /matrix

Parsing 8 months ago

delimiter: , gene_name_col: first has_header: 1 file_type: RAW_TEXT nber_cols: 2068 nber_rows: 23686

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Summary Visualization Analysis Data Compliance

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

Tutorials

Step-by-step guides for new users

File formats

Supported upload and export formats

FAQ

Frequently asked questions about ASAP

Guest Mode

Feedback

Discussions Feature requests and issues Contact us Rate the app

Back to 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

Tutorials

Step-by-step guides for new users

File formats

Supported upload and export formats

FAQ

Frequently asked questions about ASAP

Discussions

Ask questions and share ideas

Feature requests and issues

Report bugs or suggest improvements

Reach the ASAP team by email

Rate the app

Share your experience with ASAP

Guest Mode

Gene filtering #1 (basic) - Gene Metadata - _Chromosomes

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General Information

Annotation Type

Gene

Dimensions

22469 genes 1 cell

Data Type

STRING

Loom File Path

gene_filtering/713947/output.loom

Path in Loom File

/row_attrs/_Chromosomes

Produced by Analysis

Gene filtering #1

Size

351KB

Preview

22,469 values (667 unique)

Index	Value
0	9
1	19
2	20
3	11
4	14
5	16
6	11
7	__unknown
8	9
9	__unknown
10	10
11	20
12	LRG_464
13	5
14	CHR_HSCHR5_6_CTG1
15	13
16	4
17	X
18	21
19	2
20	15
21	CHR_HSCHR4_6_CTG12
22	8
23	16
24	22
25	19
26	6
27	4
28	1
29	9
30	5
31	18
32	14
33	2
34	__unknown
35	17
36	__unknown
37	__unknown
38	__unknown
39	19
40	11
41	19
42	11
43	20
44	19
45	14
46	18
47	14
48	11
49	CHR_HSCHR6_MHC_COX_CTG1
50	Y
51	6
52	13
53	LRG_588
54	3
55	10
56	16
57	__unknown
58	4
59	__unknown
60	__unknown
61	1
62	16
63	2
64	9
65	22
66	9
67	4
68	5
69	CHR_HSCHR6_MHC_COX_CTG1
70	3
71	8
72	X
73	X
74	1
75	19
76	4
77	4
78	15
79	__unknown
80	11
81	11
82	5
83	22
84	1
85	6
86	17
87	9
88	19
89	21
90	2
91	19
92	12
93	2
94	1
95	20
96	4
97	10
98	1
99	CHR_HG2066_PATCH
... and 22,369 more values