diff --git a/docs/developers.md b/docs/developers.md new file mode 100644 index 0000000..aada4bc --- /dev/null +++ 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 index b662cbb..4008dc0 100644 --- 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. \ No newline at end of file diff --git a/docs/input.md b/docs/input.md index 0f8e7f5..1c77de0 100644 --- a/docs/input.md +++ b/docs/input.md @@ -21,15 +21,23 @@ simultaneously characterizes differential expression and splicing in cohorts. The log-transformed expression of a gene with three isoforms (green, orange, and blue) is shown. The gene expression is the sum of the expression of the isoforms. Differential gene expression is modeled as two Normal distributions whose means differ by the parameter β. The proportions of the corresponding isoforms have a Dirichlet prior, and the difference in proportions between controls and cases is modeled by α (symbolized by the two triangles). An MCMC procedure is used to solve for the posterior distribution of the parameters of the model for all genes and isoforms at once. -The HBA-DEALS algorithm is explained in [Karlebach et al, 2020, Genome Biology 21:171](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02072-6). -Source code is available at the [HBA-DEALS GitHub repository](https://github.com/TheJacksonLaboratory/HBA-DEALS). +The HBA-DEALS algorithm is explained in [Karlebach et al, 2020, Genome Biology 21:171](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02072-6){:target="_blank"}. +Source code is available at the [HBA-DEALS GitHub repository](https://github.com/TheJacksonLaboratory/HBA-DEALS){:target="_blank"}. + + + +A Snakemake pipeline for running HBA-DEALS is described in the +[GitHub repository](https://github.com/TheJacksonLaboratory/covid19splicing){:target="_blank"} +for the paper [Betacoronavirus-specific alternate splicing](https://pubmed.ncbi.nlm.nih.gov/35074468/){:target="_blank"}. The GitHub repository +also contains 15 HBA-DEALS output files related to that publication that can be used as input for isopretGO. + ### Important For use with isopret, HBA-DEALS *must* be run with the ``isoform.level`` option set to true. -See the [HBADEALS documentation](https://hba-deals.readthedocs.io/en/latest/) +See the [HBADEALS documentation](https://hba-deals.readthedocs.io/en/latest/){:target="_blank"} for details. @@ -69,14 +77,19 @@ only [Ensembl](http://ensembl.org/) gene/transcript models. A Snakemake pipeline for running HBA-DEALS is described in the -[GitHub repository](https://github.com/TheJacksonLaboratory/covid19splicing) -for the paper [Betacoronavirus-specific alternate splicing](https://pubmed.ncbi.nlm.nih.gov/35074468/). The GitHub repository +[GitHub repository](https://github.com/TheJacksonLaboratory/covid19splicing){:target="_blank"} +for the paper [Betacoronavirus-specific alternate splicing](https://pubmed.ncbi.nlm.nih.gov/35074468/){:target="_blank"}. The GitHub repository also contains 15 HBA-DEALS output files related to that publication that can be used as input for Isopret-Gui. # edgeR -Alternatively [edgeR](https://pubmed.ncbi.nlm.nih.gov/19910308/) can be used to call differential expresison and alternative splicing. We provide an R script to perform the analysis +Alternatively [edgeR](https://pubmed.ncbi.nlm.nih.gov/19910308/){:target="_blank"} can be used to call differential expresison and alternative splicing. We provide an R script to perform the analysis and format the results in HBA-DEALS format (which is required to use isopret-GO): -[edgeR_output.R](../scripts/edgeR_output.R) \ No newline at end of file +[edgeR_output.R](../scripts/edgeR_output.R) + + +# DE(X)-Seq +A script is provided for DE(X)-Seq Integration for Differential Gene Expression and Transcript Usage Analysis starting from single-cell, long-read RNA-seq data to identify and quantify transcripts expressed within single cells and cell populations. +The script is available at [DEXSeq_output.R](https://github.com/TheJacksonLaboratory/isopretGO/blob/main/scripts/DEXSeq_output.R){:target="_blank"} diff --git a/docs/setup.md b/docs/setup.md index 0fe3981..f4e44cb 100644 --- a/docs/setup.md +++ b/docs/setup.md @@ -46,33 +46,5 @@ java -jar target/isopret.jar -## 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/mkdocs.yml b/mkdocs.yml index 159419b..c19168f 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -34,6 +34,8 @@ theme: nav: - Home: 'index.md' - Setup: 'setup.md' + - Input: "input.md" + - Example input files: "examples.md" - Running isopretGO: - Overview: 'running.md' - GUI: 'running-gui.md' diff --git a/package.sh b/package.sh index 5c5b562..ff628ad 100644 --- a/package.sh +++ b/package.sh @@ -74,7 +74,7 @@ function build_for_class_path() { --input "${PACKAGE_DIR}" \ --main-jar "${JAR_NAME}" \ --app-version "${VERSION}" \ - --icon "${ICON}.ico" \ + # --icon "${ICON}.ico" \ --description "${DESCRIPTION}" \ --linux-menu-group Science \ --linux-shortcut \