Skip to content

Commit d51ac35

Browse files
committed
Merge branch 'documentation' of https://github.com/pachterlab/voyager into documentation
2 parents 33fad86 + 3e8179f commit d51ac35

32 files changed

+1718
-34256
lines changed

vignettes/bivariate.ipynb

+55-1,035
Large diffs are not rendered by default.

vignettes/create_sfe.ipynb

+45-945
Large diffs are not rendered by default.

vignettes/create_sfe_v2.ipynb

+18-378
Large diffs are not rendered by default.

vignettes/localc.ipynb

+34-674
Large diffs are not rendered by default.

vignettes/multispati.ipynb

+102-1,962
Large diffs are not rendered by default.

vignettes/nonspatial.ipynb

+140-2,932
Large diffs are not rendered by default.

vignettes/preprocess_10xv3.ipynb

+22-462
Large diffs are not rendered by default.

vignettes/preprocess_atac.ipynb

+23-483
Large diffs are not rendered by default.

vignettes/preprocess_clicktag.ipynb

+22-462
Large diffs are not rendered by default.

vignettes/preprocess_crispr.ipynb

+23-483
Large diffs are not rendered by default.

vignettes/preprocess_multiome.ipynb

+23-483
Large diffs are not rendered by default.

vignettes/preprocess_nuclei.ipynb

+23-483
Large diffs are not rendered by default.

vignettes/preprocess_splitseq.ipynb

+22-462
Large diffs are not rendered by default.

vignettes/preprocess_visium.ipynb

+25-525
Large diffs are not rendered by default.

vignettes/sfemethod.ipynb

+36-736
Large diffs are not rendered by default.

vignettes/variogram.ipynb

+40-820
Large diffs are not rendered by default.

vignettes/vig10_10x_nuclei.ipynb

+13-273
Original file line numberDiff line numberDiff line change
@@ -2,27 +2,7 @@
22
"cells": [
33
{
44
"cell_type": "raw",
5-
<<<<<<< HEAD
6-
<<<<<<< HEAD
7-
<<<<<<< HEAD
8-
<<<<<<< HEAD
9-
<<<<<<< HEAD
10-
"id": "50c97000",
11-
=======
12-
"id": "45bbd170",
13-
>>>>>>> documentation-devel
14-
=======
15-
"id": "6edfad4e",
16-
>>>>>>> documentation-devel
17-
=======
18-
"id": "ef5017ab",
19-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
20-
=======
21-
"id": "6b031c45",
22-
>>>>>>> documentation-devel
23-
=======
24-
"id": "bbb257c3",
25-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
5+
"id": "c400067d",
266
"metadata": {},
277
"source": [
288
"---\n",
@@ -46,27 +26,7 @@
4626
{
4727
"cell_type": "code",
4828
"execution_count": null,
49-
<<<<<<< HEAD
50-
<<<<<<< HEAD
51-
<<<<<<< HEAD
52-
<<<<<<< HEAD
53-
<<<<<<< HEAD
54-
"id": "2f7ddd91",
55-
=======
56-
"id": "1b2a30cc",
57-
>>>>>>> documentation-devel
58-
=======
59-
"id": "ce6d2370",
60-
>>>>>>> documentation-devel
61-
=======
62-
"id": "c2ae867e",
63-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
64-
=======
65-
"id": "e7b569b7",
66-
>>>>>>> documentation-devel
67-
=======
68-
"id": "a341f1c8",
69-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
29+
"id": "6b70ccb6",
7030
"metadata": {
7131
"tags": [
7232
"remove_cell"
@@ -83,27 +43,7 @@
8343
{
8444
"cell_type": "code",
8545
"execution_count": null,
86-
<<<<<<< HEAD
87-
<<<<<<< HEAD
88-
<<<<<<< HEAD
89-
<<<<<<< HEAD
90-
<<<<<<< HEAD
91-
"id": "1e292985",
92-
=======
93-
"id": "d606361b",
94-
>>>>>>> documentation-devel
95-
=======
96-
"id": "021c965a",
97-
>>>>>>> documentation-devel
98-
=======
99-
"id": "3d32e666",
100-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
101-
=======
102-
"id": "0e4bedc6",
103-
>>>>>>> documentation-devel
104-
=======
105-
"id": "a309ad24",
106-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
46+
"id": "b173e8dc",
10747
"metadata": {
10848
"eval": false,
10949
"tags": [
@@ -138,27 +78,7 @@
13878
},
13979
{
14080
"cell_type": "markdown",
141-
<<<<<<< HEAD
142-
<<<<<<< HEAD
143-
<<<<<<< HEAD
144-
<<<<<<< HEAD
145-
<<<<<<< HEAD
146-
"id": "a79486f7",
147-
=======
148-
"id": "474720bb",
149-
>>>>>>> documentation-devel
150-
=======
151-
"id": "204068ac",
152-
>>>>>>> documentation-devel
153-
=======
154-
"id": "66cfcbbd",
155-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
156-
=======
157-
"id": "cfa68623",
158-
>>>>>>> documentation-devel
159-
=======
160-
"id": "22672e91",
161-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
81+
"id": "6082b3aa",
16282
"metadata": {},
16383
"source": [
16484
"# Introduction\n",
@@ -168,27 +88,7 @@
16888
{
16989
"cell_type": "code",
17090
"execution_count": null,
171-
<<<<<<< HEAD
172-
<<<<<<< HEAD
173-
<<<<<<< HEAD
174-
<<<<<<< HEAD
175-
<<<<<<< HEAD
176-
"id": "8dd8da34",
177-
=======
178-
"id": "8c0799c9",
179-
>>>>>>> documentation-devel
180-
=======
181-
"id": "aa0da044",
182-
>>>>>>> documentation-devel
183-
=======
184-
"id": "99674316",
185-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
186-
=======
187-
"id": "e65614d4",
188-
>>>>>>> documentation-devel
189-
=======
190-
"id": "5eadf205",
191-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
91+
"id": "6432f3cb",
19292
"metadata": {
19393
"message": false
19494
},
@@ -208,27 +108,7 @@
208108
{
209109
"cell_type": "code",
210110
"execution_count": null,
211-
<<<<<<< HEAD
212-
<<<<<<< HEAD
213-
<<<<<<< HEAD
214-
<<<<<<< HEAD
215-
<<<<<<< HEAD
216-
"id": "70d18f96",
217-
=======
218-
"id": "76a4080e",
219-
>>>>>>> documentation-devel
220-
=======
221-
"id": "c651d516",
222-
>>>>>>> documentation-devel
223-
=======
224-
"id": "3ada88a6",
225-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
226-
=======
227-
"id": "6bf489ea",
228-
>>>>>>> documentation-devel
229-
=======
230-
"id": "bb217127",
231-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
111+
"id": "b652fb67",
232112
"metadata": {
233113
"message": true,
234114
"tags": [
@@ -245,27 +125,7 @@
245125
{
246126
"cell_type": "code",
247127
"execution_count": null,
248-
<<<<<<< HEAD
249-
<<<<<<< HEAD
250-
<<<<<<< HEAD
251-
<<<<<<< HEAD
252-
<<<<<<< HEAD
253-
"id": "f69dc13f",
254-
=======
255-
"id": "731889e6",
256-
>>>>>>> documentation-devel
257-
=======
258-
"id": "70e9de2d",
259-
>>>>>>> documentation-devel
260-
=======
261-
"id": "02d505a1",
262-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
263-
=======
264-
"id": "3479ab65",
265-
>>>>>>> documentation-devel
266-
=======
267-
"id": "2d416e31",
268-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
128+
"id": "3bde125e",
269129
"metadata": {},
270130
"outputs": [],
271131
"source": [
@@ -276,27 +136,7 @@
276136
{
277137
"cell_type": "code",
278138
"execution_count": null,
279-
<<<<<<< HEAD
280-
<<<<<<< HEAD
281-
<<<<<<< HEAD
282-
<<<<<<< HEAD
283-
<<<<<<< HEAD
284-
"id": "b0a7bc10",
285-
=======
286-
"id": "cca3b205",
287-
>>>>>>> documentation-devel
288-
=======
289-
"id": "c19aa667",
290-
>>>>>>> documentation-devel
291-
=======
292-
"id": "3930f01f",
293-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
294-
=======
295-
"id": "1629f98d",
296-
>>>>>>> documentation-devel
297-
=======
298-
"id": "009117e6",
299-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
139+
"id": "75886825",
300140
"metadata": {},
301141
"outputs": [],
302142
"source": [
@@ -307,27 +147,7 @@
307147
{
308148
"cell_type": "code",
309149
"execution_count": null,
310-
<<<<<<< HEAD
311-
<<<<<<< HEAD
312-
<<<<<<< HEAD
313-
<<<<<<< HEAD
314-
<<<<<<< HEAD
315-
"id": "f7a28993",
316-
=======
317-
"id": "3b4a418f",
318-
>>>>>>> documentation-devel
319-
=======
320-
"id": "b2083d83",
321-
>>>>>>> documentation-devel
322-
=======
323-
"id": "384a311e",
324-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
325-
=======
326-
"id": "908c9379",
327-
>>>>>>> documentation-devel
328-
=======
329-
"id": "e37c6222",
330-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
150+
"id": "e65cf0ff",
331151
"metadata": {},
332152
"outputs": [],
333153
"source": [
@@ -339,27 +159,7 @@
339159
{
340160
"cell_type": "code",
341161
"execution_count": null,
342-
<<<<<<< HEAD
343-
<<<<<<< HEAD
344-
<<<<<<< HEAD
345-
<<<<<<< HEAD
346-
<<<<<<< HEAD
347-
"id": "47412c13",
348-
=======
349-
"id": "a1065699",
350-
>>>>>>> documentation-devel
351-
=======
352-
"id": "3578f305",
353-
>>>>>>> documentation-devel
354-
=======
355-
"id": "fa238000",
356-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
357-
=======
358-
"id": "3aac8e0d",
359-
>>>>>>> documentation-devel
360-
=======
361-
"id": "745e69d4",
362-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
162+
"id": "7677f5d4",
363163
"metadata": {},
364164
"outputs": [],
365165
"source": [
@@ -370,27 +170,7 @@
370170
{
371171
"cell_type": "code",
372172
"execution_count": null,
373-
<<<<<<< HEAD
374-
<<<<<<< HEAD
375-
<<<<<<< HEAD
376-
<<<<<<< HEAD
377-
<<<<<<< HEAD
378-
"id": "f6c017d0",
379-
=======
380-
"id": "a8cc700e",
381-
>>>>>>> documentation-devel
382-
=======
383-
"id": "8eb20082",
384-
>>>>>>> documentation-devel
385-
=======
386-
"id": "b2482b33",
387-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
388-
=======
389-
"id": "76d01306",
390-
>>>>>>> documentation-devel
391-
=======
392-
"id": "70796fab",
393-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
173+
"id": "abbaa7a1",
394174
"metadata": {},
395175
"outputs": [],
396176
"source": [
@@ -401,27 +181,7 @@
401181
{
402182
"cell_type": "code",
403183
"execution_count": null,
404-
<<<<<<< HEAD
405-
<<<<<<< HEAD
406-
<<<<<<< HEAD
407-
<<<<<<< HEAD
408-
<<<<<<< HEAD
409-
"id": "69ba7104",
410-
=======
411-
"id": "13c4cde5",
412-
>>>>>>> documentation-devel
413-
=======
414-
"id": "e2317085",
415-
>>>>>>> documentation-devel
416-
=======
417-
"id": "4ca4d8e7",
418-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
419-
=======
420-
"id": "d580e6c7",
421-
>>>>>>> documentation-devel
422-
=======
423-
"id": "2aac7fb6",
424-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
184+
"id": "725d18c7",
425185
"metadata": {
426186
"name": "subset-qc"
427187
},
@@ -436,27 +196,7 @@
436196
{
437197
"cell_type": "code",
438198
"execution_count": null,
439-
<<<<<<< HEAD
440-
<<<<<<< HEAD
441-
<<<<<<< HEAD
442-
<<<<<<< HEAD
443-
<<<<<<< HEAD
444-
"id": "5287f79a",
445-
=======
446-
"id": "34e278d7",
447-
>>>>>>> documentation-devel
448-
=======
449-
"id": "2662c8da",
450-
>>>>>>> documentation-devel
451-
=======
452-
"id": "fe57b0c6",
453-
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
454-
=======
455-
"id": "0c150817",
456-
>>>>>>> documentation-devel
457-
=======
458-
"id": "a8c17c34",
459-
>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4
199+
"id": "39a2d2b4",
460200
"metadata": {},
461201
"outputs": [],
462202
"source": [

0 commit comments

Comments
 (0)