Merge pull request #180 from TheJacksonLaboratory/develop

Develop
TheJacksonLaboratory · Jul 4, 2024 · d12954f · d12954f
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diff --git a/docs/developers.md b/docs/developers.md
@@ -0,0 +1,68 @@
+# Developers
+
+
+## Installable version of isopretGO (debian linux)
+
+To create an installable version of isopretGO for debian (e.g. Ubuntu) linux, run the following script (on a debian system).
+
+```
+bash package.sh
+```
+This will create a file called ``isopret-gui_1.0.0_amd64.deb``.
+
+We can install the file using this command (you may need to prepend sudo)
+
+```
+dpkg -i isopret-gui_1.0.0_amd64.deb
+```
+
+This will install an executable that can be started using this command
+
+
+```
+/opt/isopret-gui/bin/isopret-gui 
+```
+
+If desired, the executable file can be moved elsewhere. We have uploaded the  ``isopret-gui_1.0.0_amd64.deb`` file to the isopret-GO releases page.
+
+## Installable version ARM MacIntosh
+
+isopret-GO runs under Mac M1, M2, and M3. Older (intel-based) Mac systems are not supported at this time. To create an installer,
+run the same command as above.
+
+```
+bash package.sh
+```
+
+On a Mac, this command will create a file called  ``isopret-gui-1.0.0.dmg``. Double clicking this file will install a version of isopret-gui in the Applications folder.
+We have uploaded this file to the releases page.
+
+
+
+
+## Set up documentation
+
+This step is not needed to run the application, but rather describes the code we use to
+generate the isopretGO documentation.
+Enter the following code to install mkdocs and run a server with the documentation locally.
+The GitHub action will create a comparable site online.
+
+```
+python3 -m venv venv
+source venv/bin/activate
+pip install mkdocs
+pip install mkdocs-material
+pip install mkdocs-material[imaging]
+pip install mkdocs-material-extensions
+pip install pillow cairosvg
+pip install mkdocstrings[python]
+mkdocs serve
+```
+
+Note that on an M1   Mac we have encountered a difficulty with mkdocs not finding the cairo library. This can be solved
+by running
+
+```
+export DYLD_FALLBACK_LIBRARY_PATH=/opt/homebrew/lib
+```
+before running mkdocs serve.
diff --git a/docs/examples.md b/docs/examples.md
@@ -6,263 +6,15 @@ These experiments study a broad range of conditons, but they all contained two d
 samples that could be compared in a case-control design.
 
 A zip archive containing HBADEALS output files for each of the datasets can be obtained
-from the zenodo archive ([6483996](https://zenodo.org/record/6483996)).
-
-- [PMID:33524399](https://pubmed.ncbi.nlm.nih.gov/33524399/)
-- [PMID:31468702](https://pubmed.ncbi.nlm.nih.gov/31468702/)
-- [PMID:30641038](https://pubmed.ncbi.nlm.nih.gov/30641038/)
-- [PMID:33876188](https://pubmed.ncbi.nlm.nih.gov/33876188/)
-- [PMID:34413880](https://pubmed.ncbi.nlm.nih.gov/34413880/)
-- [PMID:34295332](https://pubmed.ncbi.nlm.nih.gov/34295332/)
-- [PMID:32152472](https://pubmed.ncbi.nlm.nih.gov/32152472/)
-- [PMID:30554964](https://pubmed.ncbi.nlm.nih.gov/30554964/)
-- [PMID:34669477](https://pubmed.ncbi.nlm.nih.gov/34669477/)
-- [PMID:33749664](https://pubmed.ncbi.nlm.nih.gov/33749664/)
-- [PMID:32243809](https://pubmed.ncbi.nlm.nih.gov/32243809/)
-- [PMID:30340504](https://pubmed.ncbi.nlm.nih.gov/30340504/)
-- [PMID:31829804](https://pubmed.ncbi.nlm.nih.gov/31829804/)
-- [PMID:32817457](https://pubmed.ncbi.nlm.nih.gov/32817457/)
-- [PMID:33188283](https://pubmed.ncbi.nlm.nih.gov/33188283/)
-- [PMID:30503522](https://pubmed.ncbi.nlm.nih.gov/30503522/)
-- [PMID:32487996](https://pubmed.ncbi.nlm.nih.gov/32487996/)
-- [PMID:31474574](https://pubmed.ncbi.nlm.nih.gov/31474574/)
-- [PMID:32735620](https://pubmed.ncbi.nlm.nih.gov/32735620/)
-- [PMID:32615169](https://pubmed.ncbi.nlm.nih.gov/32615169/)
-- [PMID:32441123](https://pubmed.ncbi.nlm.nih.gov/32441123/)
-- [PMID:31221130](https://pubmed.ncbi.nlm.nih.gov/31221130/)
-- [PMID:30135250](https://pubmed.ncbi.nlm.nih.gov/30135250/)
-- [PMID:33327559](https://pubmed.ncbi.nlm.nih.gov/33327559/)
-- [PMID:32294156](https://pubmed.ncbi.nlm.nih.gov/32294156/)
-- [PMID:34793334](https://pubmed.ncbi.nlm.nih.gov/34793334/)
-- [PMID:26679344](https://pubmed.ncbi.nlm.nih.gov/26679344/)
-- [PMID:34450236](https://pubmed.ncbi.nlm.nih.gov/34450236/)
-- [PMID:34215830](https://pubmed.ncbi.nlm.nih.gov/34215830/)
-- [PMID:32354235](https://pubmed.ncbi.nlm.nih.gov/32354235/)
-- [PMID:35310884](https://pubmed.ncbi.nlm.nih.gov/35310884/)
-- [PMID:24747576](https://pubmed.ncbi.nlm.nih.gov/24747576/)
-
-## Pathophysiology
-
-
-The RNA-seq datasets in this group involve investigations of diseases and disease mechanisms.
-
-.. csv-table:: pathophysiology
-   :header: "cohort", "case:control", "category", "author", "pmid"
-   :widths: 20, 20, 20, 20, 20
-
-   SRP120040_105,5:4,neurodegenerative disease,Osipovitch M (2019),30554964_
-   SRP120040_106,7:4,neurodegenerative disease,Osipovitch M (2019),30554964_
-   SRP188206_107,12:12,Neurodegenerative disease,Lavin KM (2020),31829804_
-   SRP188206_108,12:12,Neurodegenerative disease,Lavin KM (2020),31829804_
-   SRP051518_111,4:7,Kawasaki disease,Rowley AH (2015),26679344_
-   SRP051518_112,4:7,Kawasaki disease,Rowley AH (2015),26679344_
-   SRP150872_114,28:32,lupus,Davenport EE (2018),30340504_
-   SRP332552_117,12:12,diabetes,Gabriel BM (2021),34669477_
-   SRP223448_119,10:22,schizophrenia,Perez JM (2021),32152472_
-   SRP325897_221,10:12,liver pathophysiology,Lv Y (2021),34413880_
-   SRP228563_222,11:12,sickle cell disease,Creary S (2020),32487996_
-   SRP318393_244,10:10,Sjögren,Verstappen GM (2021),34295332_
-   SRP287301_247,8:13,enteric dysfunction.,Haberman Y (2021),33524399_
-   SRP144583_251,18:38,enteric fever,Blohmke CJ (2019),31468702_
-   SRP233184_261,12:12,aortic aneurysm,Chen PY (2020),32243809_
-   SRP222046_263,4:4,abdominal aortic aneurysm,Lu H (2020),32354235_
-   SRP219588_264,18:9,Vibrio vulnificus,Kim BS (2020),32817457_
-   SRP279451_265,8:8,atopic dermatitis,Möbus L (2021),32615169_
-   SRP165679_266,6:38,psoriasis,Tsoi LC (2019),30641038_
-   SRP289501_267,9:9,asthma,Helling BA (2020),33188283_
-   SRP234559_281,12:8,idiopathic aplastic anemia,Lim SP (2020),32294156_
-   SRP335222_286,18:12,basophil physiology,Puan KJ (2021),34215830_
-   SRP292025_287,6:11,neurodegenerative disease,Garofalo M (2020),33327559_
-   SRP292025_288,6:11,neurodegenerative disease,Garofalo M (2020),33327559_
-   SRP346219_294,4:4,peripheral vascular disease,Gross DA (2022),34793334_
-   SRP258588_299,12:24,Burn-McKeown syndrome,Wood KA (2020),32735620_
-   SRP262152_304,4:4,atherosclerosis,Kim JB (2020),32441123_
-   SRP305908_306,4:4,intracerebral hemorrhage,Goods BA (2021),33749664_
-   SRP040622_308,7:6,stroke,Huttner HB (2014),24747576_
-   SRP328165_310,5:8,liver pathophysiology,Zhang IW (2022),34450236_
-   SRP191103_312,8:12,gastroparesis,Herring BP (2019),31221130_
-   SRP279451_316,21:21,atopic dermatitis,Möbus L (2021),32615169_
-   SRP161727_321,9:5,Diamond-Blackfan anemia,Ulirsch JC (2018),30503522_
-   SRP134188_322,8:10,dystrophic epidermolysis bullosa,Cho RJ (2018),30135250_
-   SRP272540_323,8:6,immune thrombocytopenia,Han P (2021),33876188_
-   SRP189352_327,4:15,SF3B1 mutations,Zhang J (2019),31474574_
-   SRP342557_328,5:5,epilepsy,Gomes-Duarte A (2022),35310884_
-
-
-
-- [PMID:32652799](https://pubmed.ncbi.nlm.nih.gov/32652799/)
-- [PMID:35115664](https://pubmed.ncbi.nlm.nih.gov/35115664/)
-- [PMID:29025019](https://pubmed.ncbi.nlm.nih.gov/29025019/)
-- [PMID:32891909](https://pubmed.ncbi.nlm.nih.gov/32891909/)
-- [PMID:31827286](https://pubmed.ncbi.nlm.nih.gov/31827286/)
-- [PMID:30333485](https://pubmed.ncbi.nlm.nih.gov/30333485/)
-- [PMID:33986176](https://pubmed.ncbi.nlm.nih.gov/33986176/)
-- [PMID:34755188](https://pubmed.ncbi.nlm.nih.gov/34755188/)
-- [PMID:34739170](https://pubmed.ncbi.nlm.nih.gov/34739170/)
-- [PMID:28101782](https://pubmed.ncbi.nlm.nih.gov/28101782/)
-- [PMID:34758327](https://pubmed.ncbi.nlm.nih.gov/34758327/)
-- [PMID:30993572](https://pubmed.ncbi.nlm.nih.gov/30993572/)
-- [PMID:32710624](https://pubmed.ncbi.nlm.nih.gov/32710624/)
-- [PMID:31339449](https://pubmed.ncbi.nlm.nih.gov/31339449/)
-- [PMID:32365352](https://pubmed.ncbi.nlm.nih.gov/32365352/)
-- [PMID:34587152](https://pubmed.ncbi.nlm.nih.gov/34587152/)
-- [PMID:31941840](https://pubmed.ncbi.nlm.nih.gov/31941840/)
-- [PMID:34784250](https://pubmed.ncbi.nlm.nih.gov/34784250/)
-- [PMID:32645954](https://pubmed.ncbi.nlm.nih.gov/32645954/)
-- [PMID:34215830](https://pubmed.ncbi.nlm.nih.gov/34215830/)
-- [PMID:34886891](https://pubmed.ncbi.nlm.nih.gov/34886891/)
-- [PMID:33024153](https://pubmed.ncbi.nlm.nih.gov/33024153/)
-- [PMID:31029854](https://pubmed.ncbi.nlm.nih.gov/31029854/)
-- [PMID:32066997](https://pubmed.ncbi.nlm.nih.gov/32066997/)
-- [PMID:30367166](https://pubmed.ncbi.nlm.nih.gov/30367166/)
-
-## Physiology
-
-
-The RNA-seq datasets in this group involve investigations of physiology, cell biology, and gene regulation.
-
-.. csv-table:: physiology
-   :header: "cohort", "case:control", "category", "author", "pmid"
-   :widths: 20, 20, 20, 20, 20
-
-   SRP162188_233,9:18,DRUG-seq,Ye C (2018),30333485_
-   SRP219481_236,6:6,erythropoiesis,Rossmann MP (2021),33986176_
-   SRP117167_242,7:7,memory T cell physiology,Belarif L (2018),30367166_
-   SRP258620_243,7:5,macrophage physiology,Gutbier S (2020),32645954_
-   SRP218229_249,12:8,adipose tissue,Vijay J (2020),32066997_
-   SRP218230_253,10:6,adipose tissue,Vijay J (2020),32066997_
-   SRP260413_255,4:6,radiation damage,Brambilla F (2020),32710624_
-   SRP302877_269,4:4,proteasome,Cáceres-Gutiérrez RE (2022),34739170_
-   SRP229996_271,8:4,CD8 T cell physiology,Jansen CS (2019),31827286_
-   SRP100829_272,5:5,oocyte physiology,Reyes JM (2017),29025019_
-   SRP202034_274,5:4,liver physiology,Mendoza A (2021),34784250_
-   SRP224022_275,6:6,intestinal enteroids,Chang-Graham AL (2019),31029854_
-   SRP221491_282,4:4,basal cell-like cells,Lu J (2021),32365352_
-   SRP229589_283,4:5,tacrolimus,Dai C (2020),31941840_
-   SRP168076_285,6:6,basophil physiology,Puan KJ (2021),34215830_
-   SRP335222_286,18:12,basophil physiology,Puan KJ (2021),34215830_
-   SRP094851_293,4:4,cardiomyocyte physiology,Necela BM (2017),28101782_
-   SRP300738_295,5:5,oocyte physiology,Ntostis P (2021),34755188_
-   SRP257383_296,4:4,development,Valcourt JR (2021),34758327_
-   SRP344260_297,4:4,pericyte physiology,Rezaei-Lotfi S (2021),34886891_
-   SRP253111_303,6:6,colon physiology,Bergenheim F (2020),32891909_
-   SRP162681_307,4:4,cell cycle,Mahmoud AD (2019),31339449_
-   SRP297875_311,6:6,gene expression,Grundman J (2021),34587152_
-   SRP255876_313,8:8,exposure to formaldehyde,Gonzalez-Rivera JC (2020),33024153_
-   SRP334204_317,4:4,macrophage physiology,De M (2022),35115664_
-   SRP334204_318,4:4,macrophage physiology,De M (2022),35115664_
-   SRP334204_319,4:4,macrophage physiology,De M (2022),35115664_
-   SRP334204_320,4:4,macrophage physiology,De M (2022),35115664_
-   SRP217536_324,9:10,high-protein diet,Xu C (2020),32652799_
-   SRP149366_329,4:4,breast cells,Meng P (2019),30993572_
-
-
-- [PMID:34903601](https://pubmed.ncbi.nlm.nih.gov/34903601/)
-- [PMID:34458010](https://pubmed.ncbi.nlm.nih.gov/34458010/)
-- [PMID:32463448](https://pubmed.ncbi.nlm.nih.gov/32463448/)
-- [PMID:26566875](https://pubmed.ncbi.nlm.nih.gov/26566875/)
-- [PMID:34493867](https://pubmed.ncbi.nlm.nih.gov/34493867/)
-- [PMID:30014619](https://pubmed.ncbi.nlm.nih.gov/30014619/)
-- [PMID:34301266](https://pubmed.ncbi.nlm.nih.gov/34301266/)
-- [PMID:31048689](https://pubmed.ncbi.nlm.nih.gov/31048689/)
-- [PMID:29108258](https://pubmed.ncbi.nlm.nih.gov/29108258/)
-- [PMID:34546978](https://pubmed.ncbi.nlm.nih.gov/34546978/)
-- [PMID:34580113](https://pubmed.ncbi.nlm.nih.gov/34580113/)
-- [PMID:34986855](https://pubmed.ncbi.nlm.nih.gov/34986855/)
-- [PMID:34359754](https://pubmed.ncbi.nlm.nih.gov/34359754/)
-- [PMID:32109375](https://pubmed.ncbi.nlm.nih.gov/32109375/)
-- [PMID:29066513](https://pubmed.ncbi.nlm.nih.gov/29066513/)
-- [PMID:34238982](https://pubmed.ncbi.nlm.nih.gov/34238982/)
-- [PMID:34458146](https://pubmed.ncbi.nlm.nih.gov/34458146/)
-- [PMID:26367798](https://pubmed.ncbi.nlm.nih.gov/26367798/)
-- [PMID:24929677](https://pubmed.ncbi.nlm.nih.gov/24929677/)
-- [PMID:33203734](https://pubmed.ncbi.nlm.nih.gov/33203734/)
-- [PMID:28350380](https://pubmed.ncbi.nlm.nih.gov/28350380/)
-- [PMID:33499129](https://pubmed.ncbi.nlm.nih.gov/33499129/)
-- [PMID:34059508](https://pubmed.ncbi.nlm.nih.gov/34059508/)
-- [PMID:24176112](https://pubmed.ncbi.nlm.nih.gov/24176112/)
-- [PMID:33147339](https://pubmed.ncbi.nlm.nih.gov/33147339/)
-- [PMID:33318192](https://pubmed.ncbi.nlm.nih.gov/33318192/)
-- [PMID:30037853](https://pubmed.ncbi.nlm.nih.gov/30037853/)
-- [PMID:31843922](https://pubmed.ncbi.nlm.nih.gov/31843922/)
-- [PMID:29152775](https://pubmed.ncbi.nlm.nih.gov/29152775/)
-- [PMID:23024189](https://pubmed.ncbi.nlm.nih.gov/23024189/)
-- [PMID:33106178](https://pubmed.ncbi.nlm.nih.gov/33106178/)
-- [PMID:34270926](https://pubmed.ncbi.nlm.nih.gov/34270926/)
-- [PMID:30770362](https://pubmed.ncbi.nlm.nih.gov/30770362/)
-- [PMID:32629178](https://pubmed.ncbi.nlm.nih.gov/32629178/)
-- [PMID:32888433](https://pubmed.ncbi.nlm.nih.gov/32888433/)
-
-## Cancer
-
-
-The RNA-seq datasets in this group involve investigations of cancer.
-
-.. csv-table:: cancer
-   :header: "cohort", "case:control", "category", "author", "pmid"
-   :widths: 20, 20, 20, 20, 20
-
-   SRP219837_113,7:5,colorectal cancer,Orouji E (2022),34059508_
-   SRP065445_115,7:5,Histiocytic neoplasms,Diamond EL (2016),26566875_
-   SRP286904_223,8:8,AML,Ho JM (2020),33147339_
-   SRP090124_224,26:11,breast cancer,Pouliot MC (2017),29108258_
-   SRP215936_225,13:18,breast cancer,Arruabarrena-Aristorena A (2020),32888433_
-   SRP042620_226,42:30,breast cancer,Varley KE (2014),24929677_
-   SRP281892_227,52:26,melanoma,Hong X (2021),33203734_
-   SRP090849_228,22:9,osteosarcoma,Scott MC (2018),29066513_
-   SRP026537_229,7:15,breast cancer,Daemen A (2013),24176112_
-   SRP233497_230,21:6,pancreatic cancer,Porter RL (2019),31843922_
-   SRP331153_231,4:4,breast cancer,Arruabarrena-Aristorena A (2020),32888433_
-   SRP092413_235,26:10,neuroblastoma,Harenza JL (2017),28350380_
-   SRP217026_237,6:6,pancreatic cancer,Salvador-Barbero B (2020),32109375_
-   SRP134389_238,18:4,breast cancer,Ye IC (2018),30037853_
-   SRP247679_239,8:12,cancer,Pearson JD (2021),34270926_
-   SRP119676_240,32:30,liver cancer,Hooks KB (2018),29152775_
-   SRP111914_241,10:19,liver cancer,Li S (2019),30014619_
-   SRP050440_246,7:6,resistance to BET inhibition,Rathert P (2015),26367798_
-   SRP220467_248,8:6,retinoblastoma,Liu H (2020),33318192_
-   SRP313282_254,9:11,lung cancer,Zhang T (2021),34493867_
-   SRP012167_256,5:4,parathyroid adenoma,Haglund F (2012),23024189_
-   SRP332697_257,6:6,parathyroid adenoma,Haglund F (2012),23024189_
-   SRP332697_257,6:6,parathyroid adenoma,Haglund F (2012),23024189_
-   SRP301216_258,5:5,colorectal cancer,Hong Q (2021),34458146_
-   SRP327911_260,5:5,malignant pleomorphic adenoma,Han Z (2022),34986855_
-   SRP278517_270,11:6,ovarian cancer,Cardillo N (2021),33499129_
-   SRP303687_273,7:19,thyroid cancer,He H (2021),34238982_
-   SRP302218_277,4:4,sarcoma,Carrabotta M (2022),34903601_
-   SRP276412_278,5:5,GI stromal ,Shao Y (2021),34458010_
-   SRP183071_280,7:9,DLBCL,McCord R (2019),30770362_
-   SRP311634_284,10:10,pancreatic cancer,Farshadi EA (2021),34580113_
-   SRP183757_290,5:5,EMT-chemoresistance,Sale MJ (2019),31048689_
-   SRP267712_291,6:6,melanoma,Grigore F (2020),32629178_
-   SRP336449_292,5:12,head and neck cancer,Bouhaddou M (2021),34546978_
-   SRP253895_301,6:6,cancer,Chan TW (2020),33106178_
-   SRP253895_302,6:6,cancer,Chan TW (2020),33106178_
-   SRP226592_305,6:6,resistance phenotypes,Johnson AG (2020),32463448_
-   SRP312693_314,4:4,medulloblastoma,Rea J (2021),34359754_
-   SRP254646_315,11:11,prostate cancer,He YD (2021),34301266_
-
-- [PMID:26873097](https://pubmed.ncbi.nlm.nih.gov/26873097/)
-- [PMID:31434901](https://pubmed.ncbi.nlm.nih.gov/31434901/)
-- [PMID:33897690](https://pubmed.ncbi.nlm.nih.gov/33897690/)
-- [PMID:34128839](https://pubmed.ncbi.nlm.nih.gov/34128839/)
-- [PMID:31844885](https://pubmed.ncbi.nlm.nih.gov/31844885/)
-## Infectious disease
-
-The RNA-seq datasets in this group involve investigations of infectious disease.
-
-
-
-.. csv-table:: infectious disease
-   :header: "cohort", "case:control", "category", "author", "pmid"
-   :widths: 20, 20, 20, 20, 20
-
-   SRP049605_116,28:13,Lyme disease,Bouquet J (2016),26873097_
-   SRP286302_118,6:6,Trypanosoma cruzi,Gil-Jaramillo N (2021),33897690_
-   SRP095674_220,4:6,Schistosoma haematobium,Labuda LA (2020),31844885_
-   SRP134018_250,15:24,Tuberculous meningitis,Rohlwink UK (2019),31434901_
-   SRP320156_309,6:6,tuberculosis,Reichmann MT (2021),34128839_
+from the zenodo archive  at [10369086](https://zenodo.org/records/10369086){:target="_blanl"}.
 
+Details and PubMed identifiers for each of the experiments are available in the Supplementary material. 
 
+- Supplemental table S1: 33 disease-related cohorts
+- Supplemental table S2: 28 RNA-seq experiments devoted primarily to the study of physiology, gene expression or cell biology.
+- Supplemental table S3: 39 RNA-seq experiments devoted primarily to the study of cancer
+- Supplemental table S4: 5 RNA-seq experiments related to infectious disease.
 
 
+Additionally, the GitHub repository for the paper [Betacoronavirus-specific alternate splicing](https://pubmed.ncbi.nlm.nih.gov/35074468/)
+also contains 15 HBA-DEALS output files related to that publication that can be used as input for isopretGO.