Shiny in Bioinformatics - Bioconductor
Transcript of Shiny in Bioinformatics - Bioconductor
![Page 1: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/1.jpg)
6KLQ\�LQ�%LRLQIRUPDWLFV56WXGLR��,QF�-XO\���������
%LR&�&RQIHUHQFH
![Page 2: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/2.jpg)
6KLQ\�,QWURGXFWLRQ-RH�&KHQJ
56WXGLR��,QF�
![Page 3: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/3.jpg)
5�LV�JUHDW�
Ƚ ([FHOOHQW�IRU�VWDWLVWLFV
Ƚ $PD]LQJ�DW�GDWD�YLVXDOL]DWLRQ
Ƚ 9LEUDQW�DQG�JHQHURXV�FRPPXQLW\
![Page 4: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/4.jpg)
���EXW���
Ƚ $�SHUVRQDO�H[SHULHQFH��QRW�D�VKDUHG�RQHȽ 6KDULQJ�UHVXOWV�JHQHUDOO\�PHDQV�H[SRUWLQJ�WR�
D�VWDWLF�IRUPDWȽ 1HHG�WR�ZULWH�FRGH�WR�PDQLSXODWH�
YLVXDOL]DWLRQV�DQG�RWKHU�RXWSXWȽ 0RGHUQ�YLVXDOL]DWLRQ�LV�DQLPDWHG�DQG�
LQWHUDFWLYH�²�QRW�REYLRXV�KRZ�WR�GR�WKLV�IURP�5
![Page 5: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/5.jpg)
6KLQ\�LV5���LQWHUDFWLYLW\���ZHE
PDGH�HDV\
![Page 6: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/6.jpg)
:KDW�LV�6KLQ\"
![Page 7: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/7.jpg)
:KDW�LV�6KLQ\"
Ƚ ,QWHUDFWLYH�ZHE�DSSOLFDWLRQ�DURXQG�\RXU�5�
DQDO\VHV
Ƚ =HUR�+70/�&66�-DYD6FULSW�NQRZOHGJH�
UHTXLUHG���
Ƚ ����EXW�IXOO\�FXVWRPL]DEOH�DQG�H[WHQVLEOH�
ZLWK�+70/�&66�-DYD6FULSW
![Page 8: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/8.jpg)
:KDW�LV�6KLQ\"
Ƚ 0RGHUQ�ZHE�8,�ZLWK�DWWUDFWLYH�GHIDXOWV
Ƚ 'HVLJQHG�WR�LQWHJUDWH�ZLWK�H[LVWLQJ�
-DYD6FULSW�OLEUDULHV��LQFOXGLQJ�G��MV�
Ƚ 8VHV�D�´UHDFWLYHµ�SURJUDPPLQJ�PRGHO�
ZKLFK�DOORZV�GUDPDWLFDOO\�VLPSOHU�FRGH�
WKDQ�WUDGLWLRQDO�8,�RU�ZHE�SURJUDPPLQJ
![Page 9: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/9.jpg)
:KDW�LV�6KLQ\"
Ƚ )UHH�DQG�RSHQ�VRXUFH��*3/Y���5�SDFNDJH
Ƚ &UHDWHG�DQ�PDLQWDLQHG�E\�56WXGLR��,QF�
Ƚ )LUVW�UHOHDVHG�LQ�1RYHPEHU�����
![Page 10: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/10.jpg)
'HSOR\LQJ�6KLQ\�$SSV
Ƚ 5�SDFNDJH�LWVHOI�LV�QRW�GHVLJQHG�IRU�GHSOR\PHQW
Ƚ 6KLQ\�6HUYHU��$*3/Y��ż KWWSV���JLWKXE�FRP�UVWXGLR�VKLQ\�VHUYHU
Ƚ 6KLQ\�6HUYHU�´3URµ��&RPPHUFLDO�ż $GGV�DXWKHQWLFDWLRQ��VHFXULW\��PRQLWRULQJ�IHDWXUHV�
WR�6KLQ\�6HUYHUż &RPLQJ�VRRQ
Ƚ 6KLQ\�KRVWLQJ�RQ�UVWXGLR�FRPż &XUUHQWO\�LQ�IUHH�EHWD��VLJQ�XS�DW�KWWS���UVWXGLR�
FRP�VKLQ\
![Page 11: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/11.jpg)
6KLQ\�LQ�$FWLRQ
![Page 12: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/12.jpg)
9LVXDO�0RGHOV
KWWS���VSDUN�UVWXGLR�FRP�JHQHQWHFK�JHQHULF�UHVSRQVH�SUHGLFWLRQ�WRRO�ZHE�DSSOLFDWLRQ�GHPRQVWUDWLRQ�Y��
![Page 13: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/13.jpg)
,QWHUDFWLYH�3ORWWLQJ
KWWS���JOLPPHU�UVWXGLR�FRP�TEUF�JUQ�
![Page 14: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/14.jpg)
,QWHUDFWLYH�3ORWWLQJ
KWWS���JOLPPHU�UVWXGLR�FRP�TEUF�KHDWPDS�
![Page 15: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/15.jpg)
$QDO\WLFV�7KDW�*R�9LUDO
KWWS���VSDUN�UVWXGLR�FRP�MNDW]�6XUYH\0DSV�KWWS���ZZZ�KXIILQJWRQSRVW�FRP������������GLDOHFW�PDSVBQB��������KWPO
![Page 16: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/16.jpg)
%XLOG�3UDFWLFDO�7RROV
KWWS���JOLPPHU�UVWXGLR�FRP�V\VWHPDWLFLQ�UHWLUHPHQW�ZLWKGUDZDO�
![Page 17: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/17.jpg)
&XVWRPL]DEOH�'DVKERDUGV
KWWS���JOLPPHU�UVWXGLR�FRP�ZLQVWRQWHVW�VKLQ\�MVGHPR�
![Page 18: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/18.jpg)
&RQWURO�-DYD6FULSW�9LVXDOL]DWLRQV
KWWS���JOLPPHU�UVWXGLR�FRP�MFKHQJ�OHDIOHW�GHPR�
![Page 19: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/19.jpg)
GLVSOD\56KDZQ�%DOFRPH
8QLYHUVLW\�RI�0LQQHVRWD
![Page 20: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/20.jpg)
6KLQ\�:DONWKURXJK-HII�$OOHQ
56WXGLR��,QF�
![Page 21: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/21.jpg)
'RZQORDG�([DPSOHV
��8SGDWH�6KLQ\LQVWDOO�SDFNDJHV��GHYWRROV��OLEUDU\�GHYWRROV�LQVWDOOBJLWKXE��VKLQ\����UVWXGLR��
��'RZQORDG�([DPSOHVVRXUFH��KWWS���ELW�O\�'/%,2&��
![Page 22: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/22.jpg)
6KLQ\�([DPSOHV
Ƚ 'DWD�IURP�FXUDWHG2YDULDQ'DWD
Ƚ ���V�RI�0%�RI�PLFURDUUD\�GDWD
Ƚ :H�H[WUDFW�WZR�PDWULFHV�
ż ��1RUPDO�VDPSOHV�[���JHQHV
ż ���7XPRU�VDPSOHV�[���JHQHV
Ƚ 6WRUH�DV�([SUHVVLRQ6HW�REMHFWV
Ƚ 6DYH�DV��5GV�ILOHV
![Page 23: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/23.jpg)
([DPSOH��
Ƚ &RPSDULVRQ�RI�QRUPDO�H[SUHVVLRQ�YV��WXPRU�
H[SUHVVLRQ
Ƚ $OORZ�XVHU�WR�VHOHFW�JHQH�WR�YLVXDOL]H
Ƚ 5HQGHU�DV�ER[SORW
KWWS���ELW�O\�ELRFRQ�
![Page 24: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/24.jpg)
3UHSDUH�:RUNVSDFH
OLEUDU\�VKLQ\�RSWLRQV�VKLQ\�ODXQFK�EURZVHU )$/6(�
WXPRUQRUPDOOLEUDU\�%LREDVH�H[SUV�WXPRU�ER[SORW�OLVW�7XPRU H[SUV�WXPRU���1RUPDO H[SUV�QRUPDO���
![Page 25: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/25.jpg)
/HWV�'R�LW�
![Page 26: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/26.jpg)
'HSHQGHQF\�*UDSK���([DPSOH��
RXWSXW�JHQH3ORW
LQSXW�JHQH
UHQGHU3ORW
![Page 27: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/27.jpg)
6KLQ\�5HDFWLYLW\-RH�&KHQJ
56WXGLR��,QF�
![Page 28: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/28.jpg)
Ƚ 5HDFWLYH�SURJUDPPLQJ�LV�D�ZD\�RI�RUJDQL]LQJ�\RXU�FRGH�WKDW�HPSKDVL]HV�YDOXHV�WKDW�FDQ�FKDQJH�RYHU�WLPH���
Ƚ ���DQG�H[SUHVVLRQV�WKDW�GHSHQG�RQ�VXFK�YDOXHV���
Ƚ ���VR�WKDW�FKDQJHV�WR�WKRVH�YDOXHV�QDWXUDOO\�´IORZµ�WKURXJK�\RXU�V\VWHP�
5HDFWLYLW\
![Page 29: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/29.jpg)
5HDFWLYLW\�'HPR
![Page 30: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/30.jpg)
5HDFWLYLW\
Ƚ 5HDFWLYH�YDOXHV�DUH�YDOXHV�WKDW�YDU\�RYHU�WLPH
Ƚ 5HDFWLYH�H[SUHVVLRQV�DUH�H[SUHVVLRQV�WKDW�PD\�GHSHQG�RQ�UHDFWLYH�YDOXHV�DQG�RWKHU�UHDFWLYH�H[SUHVVLRQV
Ƚ 'HWDLOHG�H[SODQDWLRQ�LQ�WKH�WXWRULDO��KWWS���UVWXGLR�JLWKXE�LR�VKLQ\�WXWRULDO��UHDFWLYLW\�RYHUYLHZ
![Page 31: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/31.jpg)
6KLQ\�([DPSOHV��&RQWG�-HII�$OOHQ
56WXGLR��,QF�
![Page 32: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/32.jpg)
6KLQ\�([DPSOH��
Ƚ 6KLQ\�RIIHUV�WH[W�EDVHG�LQSXWV�DQG�RXWSXWV
Ƚ 9LHZ�WDEOHV
Ƚ 3ULQW�5�RXWSXW�GLUHFWO\
Ƚ /HWV�FUHDWH�DQ�DSS�WKDW�FDQ�SUHYLHZ�WKH�
JHQH�H[SUHVVLRQ�GDWD�LQ�HDFK�VHW
KWWS���ELW�O\�ELRFRQ�
![Page 33: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/33.jpg)
'HSHQGHQF\�*UDSK���([DPSOH��
RXWSXW�VXPPDU\
LQSXW�W\SH
UHQGHU3ULQW
UHQGHU7DEOHRXWSXW�YLHZLQSXW�URZV
LQSXW�FROV
![Page 34: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/34.jpg)
'HSHQGHQF\�*UDSK���([DPSOH��
RXWSXW�VXPPDU\
LQSXW�W\SH
UHQGHU3ULQW
UHQGHU7DEOHRXWSXW�YLHZLQSXW�URZV
LQSXW�FROV
H[SHQVLYH
![Page 35: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/35.jpg)
'HSHQGHQF\�*UDSK���([DPSOH��
RXWSXW�VXPPDU\
LQSXW�W\SH
UHQGHU3ULQW
UHQGHU7DEOHRXWSXW�YLHZLQSXW�URZV
LQSXW�FROV
H[SHQVLYH
![Page 36: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/36.jpg)
'HSHQGHQF\�*UDSK���([DPSOH��
RXWSXW�VXPPDU\
GDWDVHW,QSXW
UHQGHU3ULQW
UHQGHU7DEOHRXWSXW�YLHZLQSXW�URZV
LQSXW�FROV
LQSXW�W\SH
![Page 37: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/37.jpg)
'HSHQGHQF\�*UDSK���([DPSOH��
RXWSXW�VXPPDU\
GDWDVHW,QSXW
UHQGHU3ULQW
UHQGHU7DEOHRXWSXW�YLHZLQSXW�URZV
LQSXW�FROV
LQSXW�W\SH
H[SHQVLYH
![Page 38: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/38.jpg)
'HSHQGHQF\�*UDSK���([DPSOH��
RXWSXW�VXPPDU\
GDWDVHW,QSXW
UHQGHU3ULQW
UHQGHU7DEOHRXWSXW�YLHZLQSXW�URZV
LQSXW�FROV
LQSXW�W\SH
H[SHQVLYH
![Page 39: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/39.jpg)
6KLQ\�([DPSOH��
Ƚ 1R�OLPLWV�WR�FRPSXWDWLRQDO�SRZHU�RI�6KLQ\
Ƚ $Q\WKLQJ�\RX�FDQ�GR�LQ�5��\RX�FDQ�GR�LQ�
VHUYHU�5
KWWS���ELW�O\�ELRFRQ�
![Page 40: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/40.jpg)
6KLQ\�([DPSOH��
Ƚ 6KLQ\�QRW�RQO\�XVHG�LQ�LVRODWLRQ
Ƚ *UHDW�IRU�LQMHFWLQJ�VRPH�LQWHUDFWLYLW\�DW�NH\�
SRLQWV�LQ�D�ODUJHU�DQDO\VLV�ZRUNIORZ
Ƚ 8VH�VWRS$SS���WR�UHWXUQ�VRPH�GDWD�IURP�D�
6KLQ\�DSS
KWWS���ELW�O\�ELRFRQ�
![Page 41: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/41.jpg)
1H[W�6WHSV
Ƚ 6KLQ\�KRPHSDJHKWWS���UVWXGLR�FRP�VKLQ\
Ƚ 6KLQ\�7XWRULDOKWWS���UVWXGLR�JLWKXE�LR�VKLQ\�WXWRULDO
Ƚ 'LVFXVVLRQ�OLVWKWWS���JURXSV�JRRJOH�FRP�JURXS�VKLQ\�GLVFXVV
![Page 42: Shiny in Bioinformatics - Bioconductor](https://reader031.fdocuments.net/reader031/viewer/2022021207/620628958c2f7b173004fb0d/html5/thumbnails/42.jpg)
7KDQNV�4$