ydeng/bch441-work-abc-units
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
180 Commits 1 Branch 0 Tags
4d071cf8d57fc6ece7b30eeaa9d1a9ae792da79f
Go to file
Clone
Open with VS Code Open with VSCodium Open with Intellij IDEA
Download ZIP Download TAR.GZ Download BUNDLE
hyginn 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
data
New plotting reference and associated integrated dataset
2020-10-06 23:37:29 +10:00
myScripts
2020 updates and maintenance
2020-09-16 16:32:51 +10:00
scripts
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
tests
New unit: RPR-Unit_tests, with sample test file and tests directory
2017-10-15 18:46:42 -04:00
.gitignore
ignore the myScripts folder from now on
2020-09-27 00:08:31 +10:00
.myProfile.R
update process for moving .myProfile.R
2020-09-21 14:54:30 +10:00
.notes
cleanup
2019-01-07 17:51:50 +10:00
.Rprofile
BUGFIX: variable was tested before being loaded
2020-10-03 08:57:03 +10:00
.tmp.R
New workflow for Introduction
2020-09-19 22:31:06 +10:00
.utilities.R
add sealKey()
2020-10-12 09:16:52 +10:00
ABC-addSACCE_APSESproteins.R
Added and updated learning units
2017-09-12 16:09:20 -04:00
ABC-units.R
2020 updates - deactivate for maintenance
2020-09-18 21:56:30 +10:00
ABC-units.Rproj
Install files and folders
2017-08-18 22:04:01 +02:00
BIN-ALI-BLAST.R
Update script location
2020-09-25 21:50:42 +10:00
BIN-ALI-Dotplot.R
2020 updates - deactivate for maintenance
2020-09-18 21:56:30 +10:00
BIN-ALI-MSA.R
specify package when attaching BLOSUM62 - don't assume Biostrings has been loaded.
2020-10-02 20:59:29 +10:00
BIN-ALI-Optimal_sequence_alignment.R
srsly: ./myScripts/ !
2020-10-02 18:38:01 +10:00
BIN-ALI-Similarity.R
specify package when attaching BLOSUM62 - don't assume Biostrings has been loaded.
2020-10-02 20:59:29 +10:00
BIN-Data_integration.R
Updates to UniProtIDmap, and address httr/curl initialization bug
2020-09-25 02:27:42 +10:00
BIN-FUNC-Domain_annotation.R
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
BIN-FUNC-Semantic_similarity.R
Maintenance
2020-09-25 13:20:10 +10:00
BIN-MYSPE.R
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
BIN-PHYLO-Data_preparation.R
Maintenance
2020-09-26 16:45:29 +10:00
BIN-PHYLO-Tree_analysis.R
Deprecate iTol and use taxize:: instead. Rewrite of tip re-ordering.
2020-09-26 21:39:18 +10:00
BIN-PHYLO-Tree_building.R
add TOC
2020-09-26 18:22:32 +10:00
BIN-PPI-Analysis.R
style
2020-10-12 09:17:09 +10:00
BIN-SEQA-Composition.R
Maintenance. Use AACOLS.
2020-09-25 01:50:07 +10:00
BIN-Sequence.R
Maintenace, and add a Fibonacci-sequence example
2020-09-23 23:21:46 +10:00
BIN-Storing_data.R
add overlooked jsonlite:: prefix to fromJson()
2020-09-28 18:00:45 +10:00
FND-Genetic_code.R
Maintenance
2020-09-24 08:55:14 +10:00
FND-MAT-Graphs_and_networks.R
Maintenance
2020-09-23 13:00:38 +10:00
FND-STA-Information_theory.R
2020 updates - deactivate for maintenance
2020-09-18 21:56:30 +10:00
FND-STA-Probability_distribution.R
Update PPI-Analysis assets and code
2020-09-23 20:47:26 +10:00
FND-STA-Significance.R
Maintenance and sample solutions
2020-09-23 06:07:40 +10:00
functionTemplate.R
added a non-executing block for test code
2017-10-28 23:07:52 -04:00
plottingReference.R
add cex examples
2020-10-12 09:18:10 +10:00
README.md
2020 updates - deactivate for maintenance
2020-09-18 21:56:30 +10:00
RPR-Biostrings.R
Maintenance
2020-09-24 20:41:10 +10:00
RPR-ChimeraX_remote.R
return ChimeraX response invisibly and provide example of using the data for a plot
2020-09-29 14:12:11 +10:00
RPR-eUtils_XML.R
TOC, and filename typo
2020-09-25 12:03:56 +10:00
RPR-FASTA.R
update validateFASTA() logic to accommodate blanks in spacers
2020-09-26 00:43:10 +10:00
RPR-Genetic_code_optimality.R
Maintenance
2020-09-24 22:15:28 +10:00
RPR-GEO2R.R
Clarifications, and better color palettes for correlations
2020-09-25 18:51:38 +10:00
RPR-Introduction.R
New workflow for Introduction
2020-09-19 22:31:06 +10:00
RPR-PROSITE_POST.R
bugfix in dbFetchPrositeFeatures(); add return of actual motif sequence; stylistic updates
2020-09-25 11:29:28 +10:00
RPR-RegEx.R
2020 Maintenance
2020-09-22 21:02:13 +10:00
RPR-SX-PDB.R
stylisitc updates
2020-09-22 13:02:29 +10:00
RPR-UniProt_GET.R
updates; vectorized dbFetchUniProtSeq()
2020-09-25 10:47:41 +10:00
RPR-Unit_testing.R
Discuss code-local testing
2020-09-25 00:25:15 +10:00
scriptTemplate.R
Use requireNamespace(), <package>::<function>() idiom,
2019-01-08 17:11:25 +10:00

README.md

ABC-units

A Bioinformatics Course: R modules for learning units

Follow the instructions in the learning unit to install your local copy of this R-project.

Description
No description provided
Readme 7.6 MiB
Languages
R 100%