This website requires JavaScript.
7b0142afd1
Graphs and networks largely finished.
2021-12-08 01:13:01 -05:00
affe00f6fb
Line termination change and old code.
Harrison Deng
2021-11-16 00:31:48 -05:00
b1e00f52f7
Finished mutation generator.
Harrison Deng
2021-11-01 11:23:18 -04:00
a5c1c80549
Changed README.md to describe this repository.
Harrison Deng
2021-10-27 02:39:00 -04:00
a122055939
Moved work into separate file.
Harrison Deng
2021-10-27 02:35:08 -04:00
b51476f5a0
My current work.
Harrison Deng
2021-10-27 02:28:10 -04:00
25249108ca
.gitignore no longer ignores myScripts directory.
Harrison Deng
2021-10-27 02:27:17 -04:00
5e7b683323
Removed 2021 Update warning
2021-10-26 17:04:31 +02:00
4b2bab0f12
Class session notes for 2021-10-12
2021-10-19 22:44:34 +02:00
bb2e2a4c85
Revert to canonical install.packages("name") idiom
2021-10-12 12:17:53 +02:00
6939bd1e88
New script
2021-10-12 12:17:12 +02:00
c9b939b096
Typos
2021-10-05 23:48:34 +02:00
ce78612a3b
New script - illustrating the pipe
2021-10-05 22:53:41 +02:00
9603fbede8
Add troubleshooting hints via errText[[...]]
2021-10-04 22:53:06 +02:00
2e65e18f22
Unlocked (and updated)
2021-09-18 12:54:46 -04:00
5fa5dd9ff7
New retrieval logic
2021-09-18 12:36:46 -04:00
c3ca448997
Update MYSPE datasets
2021-09-18 12:36:26 -04:00
86d619ad51
rewrite getMYSPE()
2021-09-18 12:00:51 -04:00
9143b784e9
Locked out - Updates needed for 2021
2021-09-16 01:29:19 -04:00
2956ba29b5
2021 minimal maintenance
2021-09-16 01:16:22 -04:00
dd537460df
RNG seems to have changed - update a number
2021-09-16 01:05:34 -04:00
678b70ed68
First minor updates 2021
2021-09-16 00:54:29 -04:00
44209e6495
Add a line for example usage
2021-09-16 00:53:52 -04:00
65193f1e54
Minor 2021 Maintenance
2021-09-16 00:53:23 -04:00
5c577eb8d6
Small 2021 Updates
2021-09-16 00:52:14 -04:00
648925525f
style update
2021-09-15 20:54:29 -04:00
6714171102
typo
2021-09-15 20:12:10 -04:00
02ea110fe2
bugfix - wrong function name
2020-11-13 15:38:08 +10:00
33ba40a252
Bugfix in AddProtein - paste() returns deparsed expression for single-column lists...
2020-11-09 22:02:27 +10:00
39b1da5897
updates to use of "data" in nls()/nlrob()
2020-11-05 20:34:21 +10:00
1f2ec21546
Extensive additions on Poisson and Binomial distributions and NLS fits
2020-11-03 21:24:56 +10:00
7bbd19078f
Clarifications
2020-11-03 21:22:08 +10:00
7c19559839
one more palette
2020-10-21 06:14:16 +10:00
08e1803c44
Update vector ID's for betweenness centrality
2020-10-21 06:13:36 +10:00
052e148999
Removed lock-out message
2020-10-14 06:18:07 +10:00
55a0d18a66
patch a problem where jsonlite:: oversimplifies from single entries to array, rather than list.
2020-10-13 22:38:47 +10:00
d2fffdf0b8
Add code for shared protein data import
2020-10-13 22:37:31 +10:00
5524832a75
bugfix: wrong iterator
2020-10-13 21:45:14 +10:00
a50688e0d0
bugfix: jsonlite::fromJSON() chokes on a blank
2020-10-13 20:35:45 +10:00
804e3a73b7
bugfix: import all taxonomy IDs as integer
2020-10-13 20:33:04 +10:00
0541612e0b
Bugfixes
2020-10-13 20:27:56 +10:00
307aad556e
remove duplicate annotation
2020-10-13 20:26:17 +10:00
4d071cf8d5
Add code and utility functions for database export of protein annotations to JSON - towards sharing annotations on the Student Wiki Public page
2020-10-13 16:08:35 +10:00
3bee83495f
add cex examples
2020-10-12 09:18:10 +10:00
0c395a1c83
style
2020-10-12 09:17:09 +10:00
c064b34000
add sealKey()
2020-10-12 09:16:52 +10:00
a590e6d9c7
New plotting reference and associated integrated dataset
2020-10-06 23:37:29 +10:00
31c519be9f
Bugfix: called the wrong function on ENSPsel in l. 220
2020-10-04 14:11:13 +10:00
285c0db8a5
BUGFIX: variable was tested before being loaded
2020-10-03 08:57:03 +10:00
e0ff45fe94
TBC
2020-10-02 21:15:34 +10:00
efb52f636d
specify package when attaching BLOSUM62 - don't assume Biostrings has been loaded.
2020-10-02 20:59:29 +10:00
152d01273f
data in ./myScripts/
2020-10-02 18:50:36 +10:00
3173aec119
srsly: ./myScripts/ !
2020-10-02 18:38:01 +10:00
62cb8e42c1
put data in ./myScripts/
2020-10-02 18:32:29 +10:00
5ff4b3f7cb
File should be in ./myScripts/...
2020-10-02 18:31:06 +10:00
e974fbdb10
add jsonlite:: to fromjJSON() in code sample
2020-10-02 18:27:59 +10:00
d38092f08a
mRNA for Mutation-effect IA: controls
2020-10-01 18:19:59 +10:00
8839248362
Reorganized proportional plots into a "further reading" section; added nested-box, and sankey plot visualization of proportions. Introduced plotly.
2020-10-01 18:18:51 +10:00
8a5c5b3961
return taxID as name of return value
2020-10-01 11:18:08 +10:00
39417c8e60
./myScripts/.myProfile.R needs to be sourced after! .utilities.R to ensure utility functions are available.
2020-10-01 03:04:35 +10:00
9e77d948e9
return ChimeraX response invisibly and provide example of using the data for a plot
2020-09-29 14:12:11 +10:00
12e3de439f
add overlooked jsonlite:: prefix to fromJson()
2020-09-28 18:00:45 +10:00
12213b73a4
Update to student-edited file locations
2020-09-28 17:49:45 +10:00
744e762dc2
New script to demonstarte remote scripting of ChimeraX
2020-09-27 23:40:27 +10:00
df3dbb0fb6
add CX() command for ChimeraX rempote control from R-scripts.
2020-09-27 23:40:01 +10:00
0fb02b1f2f
ignore the myScripts folder from now on
2020-09-27 00:08:31 +10:00
389efcdfab
Contents for a sample .Rmd page
2020-09-27 00:07:14 +10:00
777cabcb20
Deprecate iTol and use taxize:: instead. Rewrite of tip re-ordering.
2020-09-26 21:39:18 +10:00
68b00c83e8
add TOC
2020-09-26 18:22:32 +10:00
b9ac373fce
Update - file locations and authorization of phylip apps on Mac.
2020-09-26 18:21:17 +10:00
85b7353646
ignore assignment produced data/APSEStreeRproml.rds
2020-09-26 18:20:33 +10:00
12725799e1
Maintenance
2020-09-26 16:45:29 +10:00
16513dc488
ignore assignment file data/APSESphyloSet.mfa
2020-09-26 16:45:10 +10:00
866a1c0e8f
maintenance, update file locations, minor bugs
2020-09-26 01:07:49 +10:00
092494d9de
update validateFASTA() logic to accommodate blanks in spacers
2020-09-26 00:43:10 +10:00
169ca58b92
Bugfix: q -> Q
2020-09-25 21:51:04 +10:00
091880d205
Update script location
2020-09-25 21:50:42 +10:00
092daaef97
Fix makeProteinDB.R location
2020-09-25 21:28:17 +10:00
126f956ea7
update TOC
2020-09-25 21:07:25 +10:00
85d53ae2ee
New AA colouring scheme - with better separation and transparent colours for overlapping plots. prcomp() analysis of amino acid similarity.
2020-09-25 21:06:24 +10:00
069d8136e3
Clarifications, and better color palettes for correlations
2020-09-25 18:51:38 +10:00
b42adac3f3
minor updates
2020-09-25 15:24:51 +10:00
abe30a5fb6
Maintenance
2020-09-25 13:20:10 +10:00
5a3bbc31c6
TOC, and filename typo
2020-09-25 12:03:56 +10:00
404fb05c79
minor maintenance
2020-09-25 12:01:08 +10:00
abb146f828
bugfix in dbFetchPrositeFeatures(); add return of actual motif sequence; stylistic updates
2020-09-25 11:29:28 +10:00
36140bc984
updates; vectorized dbFetchUniProtSeq()
2020-09-25 10:47:41 +10:00
2775c7c9a8
Updates to UniProtIDmap, and address httr/curl initialization bug
2020-09-25 02:27:42 +10:00
f3a436cb6e
Maintenance. Use AACOLS.
2020-09-25 01:50:07 +10:00
80079f9c5d
Discuss code-local testing
2020-09-25 00:25:15 +10:00
1002703a80
Maintenance
2020-09-24 22:15:28 +10:00
60cf30dc5a
Maintenance
2020-09-24 20:41:10 +10:00
861db60879
cleanup after adding MYSPE to .myProfile.R
2020-09-24 20:16:41 +10:00
9323c57549
bugfix
2020-09-24 19:50:39 +10:00
e55cb81f8d
validate ./scripts/myProfile, and automatically set MYSPE
2020-09-24 19:47:32 +10:00
68c5828e44
Removed vacous blanks from spacing lines
2020-09-24 18:45:47 +10:00
528dc91407
Major refactoring to simplify logic and clean code
2020-09-24 18:45:22 +10:00
f48b6bf3b7
add constants AAVALID; NUCVALID, NUCAMBIG. add AACOLS; add validateFA(); readFASTA; writeFASTA.
2020-09-24 18:43:44 +10:00
f8adefc6f9
Maintenance
2020-09-24 08:55:14 +10:00
4c793a6074
Maintenace, and add a Fibonacci-sequence example
2020-09-23 23:21:46 +10:00
Harrison Deng
Harrison Deng
hyginn