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michaelgruenstaeudl
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PACVr
Plastome Assembly Coverage Visualization in R
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Updates for Kruskal effect size reference
#49
alephnull7
closed
1 month ago
0
Refactoring of `coverage` to an R6 class & updates for outlier handling in `scripts_for_figures_tables`
#48
alephnull7
closed
1 month ago
0
Remaining questions for manuscript
#47
michaelgruenstaeudl
closed
1 month ago
2
Necessary bugfixes
#46
michaelgruenstaeudl
closed
1 month ago
1
Bugs in visualization scripts
#45
michaelgruenstaeudl
closed
1 month ago
0
Updates to tabular stats and paper figures
#44
alephnull7
closed
1 month ago
2
Necessary improvements
#43
michaelgruenstaeudl
closed
1 month ago
1
Debugging for small test datasets
#42
michaelgruenstaeudl
closed
1 month ago
0
Improving viz scripts
#41
michaelgruenstaeudl
closed
1 month ago
0
Add `depth_and_evenness_paper` procedure
#40
alephnull7
closed
1 month ago
0
Version 1.0.11
#39
alephnull7
closed
3 months ago
0
Version 1.0.10
#38
alephnull7
closed
3 months ago
1
Testing
#37
michaelgruenstaeudl
closed
4 months ago
0
Improving output plot specs
#36
michaelgruenstaeudl
closed
4 months ago
0
Improving variable and file names
#35
michaelgruenstaeudl
closed
4 months ago
0
Use `windowSize` to determine `sizeThreshold`
#34
alephnull7
closed
4 months ago
0
Use `windowSize` to determine `sizeThreshold`
#33
alephnull7
closed
4 months ago
0
Use `windowSize` to determine `sizeThreshold`
#32
alephnull7
closed
4 months ago
0
Version 1.0.8
#31
alephnull7
closed
4 months ago
0
Introduction of verbose coverage summaries
#30
alephnull7
closed
4 months ago
1
Generic `printCovStats`
#29
alephnull7
closed
4 months ago
1
Extension/Revision of function writeTables()
#28
michaelgruenstaeudl
closed
4 months ago
0
Refactor of `PACVr.complete`; decoding `IRCheck` as a single variable; handle use of `note` qualifier for IR name
#27
alephnull7
closed
5 months ago
1
Variable name change to not override existing `IRCheck`
#26
alephnull7
closed
5 months ago
0
`regionsCheck` and `syntenyLineType` as single parameter & `PACVr.verboseInformation` update
#25
alephnull7
closed
5 months ago
0
Version 1.0.7 changes documentation & GitHub action workflow for automated releases
#24
alephnull7
closed
5 months ago
1
Testing, automated documentation, GenBank string support
#23
alephnull7
closed
5 months ago
0
R-CMD-check status badge added to README.md
#22
alephnull7
closed
5 months ago
0
Mitochondrial genome compatibility; read.gb bug handling for unqualified features
#21
alephnull7
closed
5 months ago
1
Add links to DESCRIPTION + fix typo
#20
olivroy
closed
6 months ago
0
Making PACVr fit to read mitochondrial genomes
#19
michaelgruenstaeudl
closed
5 months ago
0
Move all functions that pertain to the inverted repeats ('IR') of plastid genomes or the quadripartite genome structure ('LSC, SSC, IRa, IRb') into a separate file and make their application optional. Code snippets that reside in other functions, yet deal with the inverted repeats should be converted to new functions and again made optional. Examples of existing functions that should be collected in a new file and made optional are
#18
alephnull7
closed
6 months ago
0
Optionality of IR and region analysis and visualization
#17
alephnull7
closed
6 months ago
0
Resolve the warning produced by line `rcircos.params$hist.color <- HistCol(coverage, threshold, relative, logScale)` in `PACVr.visualizeWithRCircos()`
#16
alephnull7
closed
7 months ago
0
Custom validation of histogram plot colors
#15
alephnull7
closed
7 months ago
0
Actual fix for global use of RCircos.Env?
#14
alephnull7
closed
7 months ago
0
Actual fix for RCircos.Env usage?
#13
alephnull7
closed
7 months ago
0
Use of RCircos.Env without internal library call
#12
alephnull7
closed
7 months ago
0
IMPORTANT: The package currently does not work because I disabled the internal library calls to RCircos in both`customizedRCircos.R` (occurs 2x) and `visualizeWithRCircos.R` (occurs 1x), which are no longer allowed by CRAN. However, the line `RCircosEnvironment <- RCircos::RCircos.Env` is not sufficient to get `RCircos.Env`
#11
alephnull7
closed
7 months ago
1
Some bug fixing, implementation of logger
#10
michaelgruenstaeudl
closed
7 months ago
1
Hotfix
#9
alephnull7
closed
7 months ago
0
TO DO list
#8
michaelgruenstaeudl
closed
6 months ago
1
PACVr update 2021_04_16
#7
nilsj9
closed
3 years ago
0
Importing a GBK file to create a TxDb object.
#6
DelaFuenteJavier
closed
3 years ago
1
2020_08_05_2045
#5
nilsj9
closed
3 years ago
0
PACVr Version 0.9.3 (2020.07.27)
#4
nilsj9
closed
3 years ago
0
Error with the genbank file
#3
Silverfoxcome
closed
4 years ago
13
The software tool Mosdepth was not detected on your system.
#2
Silverfoxcome
closed
4 years ago
0
what R version should I use?
#1
Silverfoxcome
closed
4 years ago
2