-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathindex-humancellatlas.html
563 lines (476 loc) · 30.9 KB
/
index-humancellatlas.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
<!DOCTYPE html>
<html lang="en">
<head>
<title>Galaxy Europe</title>
<meta property="og:title" content="" />
<meta property="og:description" content="" />
<meta property="og:image" content="/assets/media/galaxy-eu-logo.512.png" />
<meta name="description" content="The European Galaxy Instance">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<link rel="stylesheet" href="/assets/css/bootstrap.min.css">
<link rel="stylesheet" href="/assets/css/main.css">
<link rel="canonical" href="https://galaxyproject.eu/index-humancellatlas.html">
<link rel="shortcut icon" href="/assets/media/galaxy-eu-logo.64.png" type="image/x-icon" />
<link rel="alternate" type="application/rss+xml" title="Galaxy Europe" href="/feed.xml">
<link href="/assets/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous">
<script src="/assets/js/jquery-3.2.1.slim.min.js" integrity="sha256-k2WSCIexGzOj3Euiig+TlR8gA0EmPjuc79OEeY5L45g=" crossorigin="anonymous"></script>
<script src="/assets/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
</head>
<body>
<div id="wrap">
<div id="main">
<div class="container" id="maincontainer">
<div class="home">
<h1 class="no_toc" id="welcome-to-the-galaxy-human-cell-atlas-project">Welcome to the Galaxy Human Cell Atlas project</h1>
<p><img src="/assets/media/hca.png" alt="Human Cell Atlas" /></p>
<p>The <a href="https://www.humancellatlas.org" target="_blank">Human Cell Atlas</a> Galaxy setup comprises of analysis tools and workflows for the analysis of Single Cell RNA-Seq data. It includes a module that connects to the Matrix Service API of the HCA’s Data Coordination Platform that enables retrieval of gene expression matrices from any data sets in the Human Cell Atlas. The instance is based on the Galaxy framework, which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge.</p>
<p>This setup aims to give users access to as much granularity as possible in terms
of the downstream analysis steps provided by the major software for
single cell data analysis: Scanpy, SC3, Scater and Seurat. For each of these tools,
this Galaxy instance has decomposed modules for each the main functionalities:
ingestion from 10x/loom, filtering (by cells or genes), scaling, normalisation,
clustering, marker genes, and dimensionality reduction, among others. In the short
term we expect to have interoperability between these tools through the Loom exchange format.
Additionally, we provide specialised viewers for single cell clustering data:
UCSC CellBrowser and cellxgene interactive tool (contributed by the great Galaxy community).</p>
<p>Tools available under HCA-Single Cell section were mainly brought to Galaxy by
the <a href="https://www.ebi.ac.uk/about/people/irene-papatheodorou" target="_blank">Gene Expression Team</a>
at <a href="https://www.ebi.ac.uk" target="_blank">EMBL-EBI</a> and the <a href="https://www.sanger.ac.uk/science/groups/teichmann-group" target="_blank">Teichmann Team</a> at the <a href="https://www.sanger.ac.uk/" target="_blank">Wellcome Sanger Institute</a>.</p>
<h1 class="no_toc" id="content">Content</h1>
<ol id="markdown-toc">
<li><a href="#get-started" id="markdown-toc-get-started">Get started</a></li>
<li><a href="#available-workflows" id="markdown-toc-available-workflows">Available Workflows</a></li>
<li><a href="#available-tools" id="markdown-toc-available-tools">Available tools</a> <ol>
<li><a href="#single-cell-galaxy-tools-developed-for-the-human-cell-atlas" id="markdown-toc-single-cell-galaxy-tools-developed-for-the-human-cell-atlas">Single Cell Galaxy Tools developed for the Human Cell Atlas</a></li>
</ol>
</li>
<li><a href="#contributors" id="markdown-toc-contributors">Contributors</a></li>
</ol>
<h1 id="get-started">Get started</h1>
<p>Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take <a href="https://humancellatlas.usegalaxy.eu/tours/core.galaxy_ui" target="_blank">a guided tour</a> through Galaxy’s user interface.</p>
<h1 id="available-workflows">Available Workflows</h1>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Workflow</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/u/pmoreno/w/humancellatlas-scanpy-cellbrowser" target="_blank">Human Cell Atlas - Scanpy - CellBrowser</a></td>
<td>Retrieve data from the Human Cell Atlas matrix service, analysis with Scanpy and visualisation with UCSC CellBrowser</td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/u/pmoreno/w/atlas-scanpy-cellbrowser-imported-from-uploaded-file" target="_blank">EBI Single Cell Expression Atlas - Scanpy - CellBrowser</a></td>
<td>Retrieve expression matrices from Single Cell Expression Atlas, analysis with Scanpy and visualisation with UCSC CellBrowser</td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/u/pmoreno/w/scanpy-prod-13-smart-imported-from-uploaded-file" target="_blank">EBI Single Cell Expression Atlas Scanpy Prod 1.3</a></td>
<td>Workflow used for clustering data in the <a href="https://www.ebi.ac.uk/gxa/sc/release-notes.html" target="_blank">release 6 to 9</a> of <a href="https://www.ebi.ac.uk/gxa/sc/home" target="_blank">Single Cell Expression Atlas</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/u/pmoreno/w/ebi-sc-expression-atlas-release-10-analysis-pipeline-scanpy-143" target="_blank">EBI Single Cell Expression Atlas Tertiary Analysis Rel 10</a></td>
<td>Workflow used for clustering data in the <a href="https://www.ebi.ac.uk/gxa/sc/release-notes.html" target="_blank">release 10</a> of <a href="https://www.ebi.ac.uk/gxa/sc/home" target="_blank">Single Cell Expression Atlas</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/u/pmoreno/w/ebi-sc-expression-atlas-release-11-analysis-pipeline" target="_blank">EBI Single Cell Expression Atlas Tertiary Analysis Rel 11</a></td>
<td>Workflow used for clustering data in the <a href="https://www.ebi.ac.uk/gxa/sc/release-notes.html" target="_blank">releases 11 and 12</a> of <a href="https://www.ebi.ac.uk/gxa/sc/home" target="_blank">Single Cell Expression Atlas</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/u/pmoreno/w/ebi-sc-expression-atlas-release-13-analysis-pipeline-scanpy-160---harmony-batch-correction" target="_blank">EBI Single Cell Expression Atlas Tertiary Analysis Rel 13</a></td>
<td>Workflow used for downstream analysis in the <a href="https://www.ebi.ac.uk/gxa/sc/release-notes.html" target="_blank">releases 13 to 15</a> of <a href="https://www.ebi.ac.uk/gxa/sc/home" target="_blank">Single Cell Expression Atlas</a>.</td>
</tr>
</tbody>
</table>
<h1 id="available-tools">Available tools</h1>
<p>In this section we list all tools that have been integrated in the RNA workbench. The list is likely to grow as soon as further tools and workflows are contributed. To ease readability, we divided them into categories.</p>
<h2 id="single-cell-galaxy-tools-developed-for-the-human-cell-atlas">Single Cell Galaxy Tools developed for the Human Cell Atlas</h2>
<h3 id="data-retrieval-from-single-cell-data-repositories">Data retrieval from Single Cell data Repositories</h3>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Tool</th>
<th>Description</th>
<th>Reference</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/hca_matrix_downloader/hca_matrix_downloader" target="_top" title="hca_matrix_downloader">hca_matrix_downloader</a></td>
<td>Human Cell Atlas Matrix Downloader retrieves expression matrices and metadata from the Human Cell Atlas.</td>
<td><a href="https://arxiv.org/abs/1810.05192" target="_blank">Regev et al. 2018</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa" target="_top" title="retrieve_scxa">retrieve_scxa</a></td>
<td>EBI SCXA Data Retrieval downloads expression matrices and metadata from the EBI Single Cell Expression Atlas (SCXA)</td>
<td><a href="https://doi.org/10.1093/nar/gkx1158" target="_blank">Papatheodorou et al. 2018</a></td>
</tr>
</tbody>
</table>
<p>10x files produced by these tools can be consumed by 10x reader modules in the tools below.</p>
<h3 id="visualisation">Visualisation</h3>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Tool</th>
<th>Description</th>
<th>Reference</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/ucsc_cell_browser/ucsc_cell_browser" target="_top" title="ucsc_cell_browser">ucsc_cell_browser</a></td>
<td>UCSC Cell Browser displays single-cell clusterized data in an interactive web application.</td>
<td><a href="https://cells.ucsc.edu/" target="_blank">cells.ucsc.edu</a></td>
</tr>
</tbody>
</table>
<h3 id="scanpy">Scanpy</h3>
<p>Granular tools for accessing the main Scanpy functionalities.</p>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Tool</th>
<th>Description</th>
<th>Reference</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x" target="_top" title="scanpy_read_10x">scanpy_read_10x</a></td>
<td>Scanpy Read10x into hdf5 object handled by scanpy</td>
<td><a href="https://doi.org/10.1186/s13059-017-1382-0" target="_blank">Wolf et al. 2018</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes" target="_top" title="scanpy_filter_genes">scanpy_filter_genes</a></td>
<td>Scanpy FilterGenes based on counts and numbers of cells expressed</td>
<td><a href="https://doi.org/10.1186/s13059-017-1382-0" target="_blank">Wolf et al. 2018</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells" target="_top" title="scanpy_filter_cells">scanpy_filter_cells</a></td>
<td>Scanpy FilterCells based on counts and numbers of genes expressed</td>
<td><a href="https://doi.org/10.1186/s13059-017-1382-0" target="_blank">Wolf et al. 2018</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data" target="_top" title="scanpy_normalise_data">scanpy_normalise_data</a></td>
<td>Scanpy NormaliseData to make all cells having the same total expression</td>
<td><a href="https://doi.org/10.1186/s13059-017-1382-0" target="_blank">Wolf et al. 2018</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes" target="_top" title="scanpy_find_variable_genes">scanpy_find_variable_genes</a></td>
<td>Scanpy FindVariableGenes based on normalised dispersion of expression</td>
<td><a href="https://doi.org/10.1186/s13059-017-1382-0" target="_blank">Wolf et al. 2018</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data" target="_top" title="scanpy_scale_data">scanpy_scale_data</a></td>
<td>Scanpy ScaleData to make expression variance the same for all genes</td>
<td><a href="https://doi.org/10.1186/s13059-017-1382-0" target="_blank">Wolf et al. 2018</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca" target="_top" title="scanpy_run_pca">scanpy_run_pca</a></td>
<td>Scanpy RunPCA for dimensionality reduction</td>
<td><a href="https://doi.org/10.1186/s13059-017-1382-0" target="_blank">Wolf et al. 2018</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph" target="_top" title="scanpy_compute_graph">scanpy_compute_graph</a></td>
<td>Scanpy ComputeGraph to derive kNN graph</td>
<td><a href="https://doi.org/10.1186/s13059-017-1382-0" target="_blank">Wolf et al. 2018</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster" target="_top" title="scanpy_find_cluster">scanpy_find_cluster</a></td>
<td>Scanpy FindCluster based on community detection on KNN graph</td>
<td><a href="https://doi.org/10.1186/s13059-017-1382-0" target="_blank">Wolf et al. 2018</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers" target="_top" title="scanpy_find_markers">scanpy_find_markers</a></td>
<td>Scanpy FindMarkers to find differentially expressed genes between groups</td>
<td><a href="https://doi.org/10.1186/s13059-017-1382-0" target="_blank">Wolf et al. 2018</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne" target="_top" title="scanpy_run_tsne">scanpy_run_tsne</a></td>
<td>Scanpy RunTSNE visualise cell clusters using tSNE</td>
<td><a href="https://doi.org/10.1186/s13059-017-1382-0" target="_blank">Wolf et al. 2018</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap" target="_top" title="scanpy_run_umap">scanpy_run_umap</a></td>
<td>Scanpy RunUMAP visualise cell clusters using UMAP</td>
<td><a href="https://doi.org/10.1186/s13059-017-1382-0" target="_blank">Wolf et al. 2018</a></td>
</tr>
</tbody>
</table>
<h3 id="seurat">Seurat</h3>
<p>Granular tools for accessing the main Seurat functionalities. These tools received contributions from Maria Doyle <a href="https://github.com/mblue9">@mblue9</a>.</p>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Tool</th>
<th>Description</th>
<th>Reference</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x" target="_top" title="seurat_read10x">seurat_read10x</a></td>
<td>Seurat Read10x Loads 10x data into a serialized seurat R object</td>
<td><a href="https://doi.org/10.1038/nbt.3192" target="_blank">Satija et al. 2015</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_create_seurat_object/seurat_create_seurat_object" target="_top" title="seurat_create_seurat_object">seurat_create_seurat_object</a></td>
<td>Seurat CreateSeuratObject create a Seurat object</td>
<td><a href="https://doi.org/10.1038/nbt.3192" target="_blank">Satija et al. 2015</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells" target="_top" title="seurat_filter_cells">seurat_filter_cells</a></td>
<td>Seurat FilterCells filter cells in a Seurat object</td>
<td><a href="https://doi.org/10.1038/nbt.3192" target="_blank">Satija et al. 2015</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data" target="_top" title="seurat_normalise_data">seurat_normalise_data</a></td>
<td>Seurat NormaliseData normalise data</td>
<td><a href="https://doi.org/10.1038/nbt.3192" target="_blank">Satija et al. 2015</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes" target="_top" title="seurat_find_variable_genes">seurat_find_variable_genes</a></td>
<td>Seurat FindVariableGenes identify variable genes</td>
<td><a href="https://doi.org/10.1038/nbt.3192" target="_blank">Satija et al. 2015</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data" target="_top" title="seurat_scale_data">seurat_scale_data</a></td>
<td>Seurat ScaleData scale and center genes</td>
<td><a href="https://doi.org/10.1038/nbt.3192" target="_blank">Satija et al. 2015</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca" target="_top" title="seurat_run_pca">seurat_run_pca</a></td>
<td>Seurat RunPCA run a PCA dimensionality reduction</td>
<td><a href="https://doi.org/10.1038/nbt.3192" target="_blank">Satija et al. 2015</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters" target="_top" title="seurat_find_clusters">seurat_find_clusters</a></td>
<td>Seurat FindClusters find clusters of cells</td>
<td><a href="https://doi.org/10.1038/nbt.3192" target="_blank">Satija et al. 2015</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_markers/seurat_find_markers" target="_top" title="seurat_find_markers">seurat_find_markers</a></td>
<td>Seurat FindMarkers find markers (differentially expressed genes)</td>
<td><a href="https://doi.org/10.1038/nbt.3192" target="_blank">Satija et al. 2015</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_dim_plot/seurat_dim_plot" target="_top" title="seurat_dim_plot">seurat_dim_plot</a></td>
<td>Seurat Plot dimension reduction graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.</td>
<td><a href="https://doi.org/10.1038/nbt.3192" target="_blank">Satija et al. 2015</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne" target="_top" title="seurat_run_tsne">seurat_run_tsne</a></td>
<td>Seurat RunTSNE run t-SNE dimensionality reduction</td>
<td><a href="https://doi.org/10.1038/nbt.3192" target="_blank">Satija et al. 2015</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_export_cellbrowser/seurat_export_cellbrowser" target="_top" title="seurat_export_cellbrowser">seurat_export_cellbrowser</a></td>
<td>Seurat Export2CellBrowser produces files for UCSC CellBrowser import.</td>
<td><a href="https://doi.org/10.1038/nbt.3192" target="_blank">Satija et al. 2015</a></td>
</tr>
</tbody>
</table>
<h3 id="scater">Scater</h3>
<p>Granular tools for accessing the main Scater functionalities. Normally used in combination with SC3.</p>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Tool</th>
<th>Description</th>
<th>Reference</th>
</tr>
</thead>
<tbody>
<tr>
<td><b>Unknown Tool</b></td>
<td>Scater read 10x data Loads 10x data into a serialized scater R object</td>
<td><a href="https://doi.org/10.1093/bioinformatics/btw777" target="_blank">McCarthy et al. 2017</a></td>
</tr>
<tr>
<td><b>Unknown Tool</b></td>
<td>Scater CalculateQcMetrics based on expression values and experiment information</td>
<td><a href="https://doi.org/10.1093/bioinformatics/btw777" target="_blank">McCarthy et al. 2017</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter" target="_top" title="scater_filter">scater_filter</a></td>
<td>Scater Filter cells and genes based on pre-calculated stats and QC metrics</td>
<td><a href="https://doi.org/10.1093/bioinformatics/btw777" target="_blank">McCarthy et al. 2017</a></td>
</tr>
<tr>
<td><b>Unknown Tool</b></td>
<td>Scater DetectOutlier cells based on expression metrics</td>
<td><a href="https://doi.org/10.1093/bioinformatics/btw777" target="_blank">McCarthy et al. 2017</a></td>
</tr>
<tr>
<td><b>Unknown Tool</b></td>
<td>Scater CalculateCPM from raw counts</td>
<td><a href="https://doi.org/10.1093/bioinformatics/btw777" target="_blank">McCarthy et al. 2017</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize" target="_top" title="scater_normalize">scater_normalize</a></td>
<td>Scater Normalise expression values by library size in log2 scale</td>
<td><a href="https://doi.org/10.1093/bioinformatics/btw777" target="_blank">McCarthy et al. 2017</a></td>
</tr>
</tbody>
</table>
<h3 id="sc3">SC3</h3>
<p>Granular tools for accessing the main SC3 functionalities. Normally used in combination with Scater.</p>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Tool</th>
<th>Description</th>
<th>Reference</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/sc3_prepare/sc3_prepare" target="_top" title="sc3_prepare">sc3_prepare</a></td>
<td>SC3 Prepare a sc3 SingleCellExperiment object</td>
<td><a href="https://doi.org/10.1038/nmeth.4236" target="_blank">Kisilev et al. 2017</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/sc3_calc_consens/sc3_calc_consens" target="_top" title="sc3_calc_consens">sc3_calc_consens</a></td>
<td>SC3 Calculate Consensus from multiple runs of k-means clustering</td>
<td><a href="https://doi.org/10.1038/nmeth.4236" target="_blank">Kisilev et al. 2017</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/sc3_calc_transfs/sc3_calc_transfs" target="_top" title="sc3_calc_transfs">sc3_calc_transfs</a></td>
<td>SC3 Calculate Transformations of distances using PCA and graph Laplacian</td>
<td><a href="https://doi.org/10.1038/nmeth.4236" target="_blank">Kisilev et al. 2017</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/sc3_calc_biology/sc3_calc_biology" target="_top" title="sc3_calc_biology">sc3_calc_biology</a></td>
<td>SC3 DiffExp calculates DE genes, marker genes and cell outliers</td>
<td><a href="https://doi.org/10.1038/nmeth.4236" target="_blank">Kisilev et al. 2017</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/sc3_estimate_k/sc3_estimate_k" target="_top" title="sc3_estimate_k">sc3_estimate_k</a></td>
<td>SC3 Estimate the number of clusters for k-means clustering</td>
<td><a href="https://doi.org/10.1038/nmeth.4236" target="_blank">Kisilev et al. 2017</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/sc3_calc_dists/sc3_calc_dists" target="_top" title="sc3_calc_dists">sc3_calc_dists</a></td>
<td>SC3 Calculate Distances between cells</td>
<td><a href="https://doi.org/10.1038/nmeth.4236" target="_blank">Kisilev et al. 2017</a></td>
</tr>
<tr>
<td><a href="https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/sc3_kmeans/sc3_kmeans" target="_top" title="sc3_kmeans">sc3_kmeans</a></td>
<td>SC3 K-Means perform k-means clustering</td>
<td><a href="https://doi.org/10.1038/nmeth.4236" target="_blank">Kisilev et al. 2017</a></td>
</tr>
</tbody>
</table>
<p>…plus all the great tools normally available at the <a href="https://usegalaxy.eu/">usegalaxy.eu</a>.</p>
<h1 id="contributors">Contributors</h1>
<ul>
<li><a href="https://github.com/pcm32">Pablo Moreno</a></li>
<li><a href="https://github.com/nh3">Ni Huang</a></li>
<li><a href="https://github.com/pinin4fjords">Jonathan Manning</a></li>
<li><a href="https://github.com/a-solovyev12">Andrey Solovyev</a></li>
<li><a href="https://github.com/cartal">Carlos Talavera-Lopez</a></li>
<li><a href="https://github.com/suhaibMo">Suhaib Mohammed</a></li>
<li><a href="https://twitter.com/irenepapatheodo">Irene Papatheodorou</a></li>
<li><a href="https://github.com/bgruening/">Björn Gruening</a></li>
<li><a href="https://github.com/ktpolanski">Krzysztof Polanski</a></li>
<li><a href="https://github.com/mblue9/">Maria Doyle</a></li>
</ul>
<h2>Our Data Policy</h2>
<table class="table table-striped">
<thead>
<tr>
<th>Registered Users</th><th>Unregistered Users</th><th>FTP Data</th><th>GDPR Compliance</th>
</tr>
</thead>
<tbody>
<tr>
<td>User data on UseGalaxy.eu (i.e. datasets, histories) will be available as long
as they are not deleted by the user. Once marked as deleted the datasets will
be permanently removed within 14 days. If the user "purges" the dataset in the
Galaxy, it will be removed immediately, permanently.
An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a>
for a limited time period in special cases.
</td>
<td>Processed data will only be accessible during one browser session, using a
cookie to identify your data. This cookie is not used for any other purposes
(e.g. tracking or analytics).
If UseGalaxy.eu service is not accessed for 90 days, those datasets will be
permanently deleted.
</td>
<td>Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon
as possible. Data left in FTP folders for more than 3 months, will be deleted.
</td>
<td>The Galaxy service complies with the EU General Data Protection Regulation
(GDPR). You can read more about this on our
<a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>.</td>
</tr>
</tbody>
</table>
<!-- <h4>Registered Users</h4>
User data on UseGalaxy.eu (i.e. datasets, histories) will be available as long
as they are not deleted by the user. Once marked as deleted the datasets will
be permanently removed within 14 days. If the user "purges" the dataset in the
Galaxy, it will be removed immediately, permanently.
An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a>
for a limited time period in special cases.
<h4>Unregistered Users</h4>
Processed data will only be accessible during one browser session, using a
cookie to identify your data. This cookie is not used for any other purposes
(e.g. tracking or analytics).
If UseGalaxy.eu service is not accessed for 90 days, those datasets will be
permanently deleted.
<h4>FTP Data</h4>
Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon
as possible. Data left in FTP folders for more than 3 months, will be deleted.
<h4>GDPR Compliance</h4>
The Galaxy service complies with the EU General Data Protection Regulation
(GDPR). You can read more about this on our
<a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>.
-->
<div>
<iframe style="border: 0px" width="100%" height="150px" src="https://stats.galaxyproject.eu/d-solo/000000034/jobs-dashboard?orgId=1&refresh=1m&panelId=1" ></iframe>
</div>
<div>
<!--<iframe style="border: 0px" width="33%" height="100px" src="https://stats.galaxyproject.eu/d-solo/000000034/jobs-dashboard?orgId=1&refresh=1m&panelId=3" ></iframe>-->
</div>
<div class="row">
<section class="section-content">
<div class="col-md-12">
</div>
</section>
</div>
</div>
</div>
</div>
</div>
<footer class="navbar-default">
<div class="container">
<div class="row">
</div>
<div class="row">
<div class="col-lg-12" style="text-align:center">
<p>UseGalaxy.eu is maintained largely by the <a href="/freiburg/">Freiburg Galaxy Team</a> but also collectively by groups and individuals from across Europe. All of the member sites in this repository contribute to the European Galaxy Project.
For <strong>acknowledgement</strong>, please refer to the <a href="/about">About</a> section.
All content on this site is available under <a href="https://creativecommons.org/share-your-work/public-domain/cc0/">CC0-1.0</a> unless otherwise specified.</p>
</div>
</div>
<div class="row">
<div class="col-lg-12" style="text-align:center">
<ul class="contact-info">
<li><i class="fa fa-github"></i><a href="https://github.com/usegalaxy-eu/website/tree/master/index-humancellatlas.md">Edit this page on GitHub</a></li>
<li><i class="fa fa-envelope"></i><a href="mailto:[email protected]">[email protected]</a></li>
<li><i class="fa fa-github"></i><a href="https://github.com/usegalaxy-eu">usegalaxy-eu</a></li>
<li><img class="fa-mastodon" src="/assets/media/mastodon.svg" style="width:18px;height:18px;padding-right:4px;filter:grayscale(100%);-webkit-filter:grayscale(100%);"/><a href="https://bawü.social/@galaxyfreiburg">galaxyfreiburg</a></li>
<li><i class="fa fa-rss"></i>Subscribe <a href="/feed.xml">via RSS (UseGalaxy.eu Feed)</a></li>
</ul>
</div>
</div>
</div>
</footer>
<script async defer data-domain="galaxyproject.eu" src="https://plausible.galaxyproject.eu/js/plausible.js"></script>
</body>
</html>