michaelgruenstaeudl PACVr issues

michaelgruenstaeudl / PACVr

Plastome Assembly Coverage Visualization in R

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Summarizing and visualizing the regression-based statistical tests

#51 michaelgruenstaeudl opened 1 month ago
6
Initial regression analysis file

#50 alephnull7 closed 1 month ago
0
Updates for Kruskal effect size reference

#49 alephnull7 closed 5 months ago
0
Refactoring of `coverage` to an R6 class & updates for outlier handling in `scripts_for_figures_tables`

#48 alephnull7 closed 5 months ago
0
Remaining questions for manuscript

#47 michaelgruenstaeudl closed 6 months ago
2
Necessary bugfixes

#46 michaelgruenstaeudl closed 6 months ago
1
Bugs in visualization scripts

#45 michaelgruenstaeudl closed 6 months ago
0
Updates to tabular stats and paper figures

#44 alephnull7 closed 6 months ago
2
Necessary improvements

#43 michaelgruenstaeudl closed 6 months ago
1
Debugging for small test datasets

#42 michaelgruenstaeudl closed 6 months ago
0
Improving viz scripts

#41 michaelgruenstaeudl closed 6 months ago
0
Add `depth_and_evenness_paper` procedure

#40 alephnull7 closed 6 months ago
0
Version 1.0.11

#39 alephnull7 closed 7 months ago
0
Version 1.0.10

#38 alephnull7 closed 8 months ago
1
Testing

#37 michaelgruenstaeudl closed 9 months ago
0
Improving output plot specs

#36 michaelgruenstaeudl closed 9 months ago
0
Improving variable and file names

#35 michaelgruenstaeudl closed 9 months ago
0
Use `windowSize` to determine `sizeThreshold`

#34 alephnull7 closed 9 months ago
0
Use `windowSize` to determine `sizeThreshold`

#33 alephnull7 closed 9 months ago
0
Use `windowSize` to determine `sizeThreshold`

#32 alephnull7 closed 9 months ago
0
Version 1.0.8

#31 alephnull7 closed 9 months ago
0
Introduction of verbose coverage summaries

#30 alephnull7 closed 9 months ago
1
Generic `printCovStats`

#29 alephnull7 closed 9 months ago
1
Extension/Revision of function writeTables()

#28 michaelgruenstaeudl closed 9 months ago
0
Refactor of `PACVr.complete`; decoding `IRCheck` as a single variable; handle use of `note` qualifier for IR name

#27 alephnull7 closed 9 months ago
1
Variable name change to not override existing `IRCheck`

#26 alephnull7 closed 9 months ago
0
`regionsCheck` and `syntenyLineType` as single parameter & `PACVr.verboseInformation` update

#25 alephnull7 closed 9 months ago
0
Version 1.0.7 changes documentation & GitHub action workflow for automated releases

#24 alephnull7 closed 9 months ago
1
Testing, automated documentation, GenBank string support

#23 alephnull7 closed 10 months ago
0
R-CMD-check status badge added to README.md

#22 alephnull7 closed 10 months ago
0
Mitochondrial genome compatibility; read.gb bug handling for unqualified features

#21 alephnull7 closed 10 months ago
1
Add links to DESCRIPTION + fix typo

#20 olivroy closed 10 months ago
0
Making PACVr fit to read mitochondrial genomes

#19 michaelgruenstaeudl closed 10 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 10 months ago
0
Optionality of IR and region analysis and visualization

#17 alephnull7 closed 10 months ago
0
Resolve the warning produced by line `rcircos.params$hist.color <- HistCol(coverage, threshold, relative, logScale)` in `PACVr.visualizeWithRCircos()`

#16 alephnull7 closed 11 months ago
0
Custom validation of histogram plot colors

#15 alephnull7 closed 11 months ago
0
Actual fix for global use of RCircos.Env?

#14 alephnull7 closed 11 months ago
0
Actual fix for RCircos.Env usage?

#13 alephnull7 closed 11 months ago
0
Use of RCircos.Env without internal library call

#12 alephnull7 closed 11 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 11 months ago
1
Some bug fixing, implementation of logger

#10 michaelgruenstaeudl closed 11 months ago
1
Hotfix

#9 alephnull7 closed 1 year ago
0
TO DO list

#8 michaelgruenstaeudl closed 10 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 4 years ago
1
2020_08_05_2045

#5 nilsj9 closed 4 years ago
0
PACVr Version 0.9.3 (2020.07.27)

#4 nilsj9 closed 4 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