Package: LinTInd 1.11.0
Luyue Wang
LinTInd: Lineage tracing by indels
When we combine gene-editing technology and sequencing technology, we need to reconstruct a lineage tree from alleles generated and calculate the similarity between each pair of groups. FindIndel() and IndelForm() function will help you align each read to reference sequence and generate scar form strings respectively. IndelIdents() function will help you to define a scar form for each cell or read. IndelPlot() function will help you to visualize the distribution of deletion and insertion. TagProcess() function will help you to extract indels for each cell or read. TagDist() function will help you to calculate the similarity between each pair of groups across the indwells they contain. BuildTree() function will help you to reconstruct a tree. PlotTree() function will help you to visualize the tree.
Authors:
LinTInd_1.11.0.tar.gz
LinTInd_1.11.0.zip(r-4.5)LinTInd_1.11.0.zip(r-4.4)LinTInd_1.11.0.zip(r-4.3)
LinTInd_1.11.0.tgz(r-4.4-any)LinTInd_1.11.0.tgz(r-4.3-any)
LinTInd_1.11.0.tar.gz(r-4.5-noble)LinTInd_1.11.0.tar.gz(r-4.4-noble)
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LinTInd.pdf |LinTInd.html✨
LinTInd/json (API)
NEWS
| # Install 'LinTInd' in R: |
| install.packages('LinTInd', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- cellsinfo - Example of cellsinfo
- celltype - Example of celltype
- cutsite - Example of cutsite
- data - Example of data
- ref - Example of ref
- scarform - Example of scarform
- scarinfo - Example of scarinfo
- scarref - Example of scarref
- scarref_all - Example of scarref_all
- tag - Example of tag
- treeinfo - Example of treeinfo
On BioConductor:LinTInd-1.9.0(bioc 3.20)LinTInd-1.8.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 23 days agofrom:7c091a55bd. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:align_to_rangeBuildTreechange_form_statFindIndelIndelFormIndelIdentsIndelPlotPlotTreeReadCutsiteReadFastaTagDistTagProcess
Dependencies:apeaplotaskpassbase64encBiocGenericsBiostringsbslibcachemclicolorspacecowplotcpp11crayoncurldata.tabledata.treedigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataggfunggnewscaleggplot2ggplotifyggtreegluegridGraphicsgtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnetworkD3nlmeopensslpatchworkpheatmappillarpkgconfigplyrpurrrpwalignR6rappdirsRColorBrewerRcppreshape2rlangrlistrmarkdownS4VectorssassscalesstringdiststringistringrsystibbletidyrtidyselecttidytreetinytextreeioUCSC.utilsutf8vctrsviridisLitewithrxfunXMLXVectoryamlyulab.utilszlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| align_to_range | align_to_range |
| BuildTree | BuildTree |
| example of cellsinfo | cellsinfo |
| example of celltype | celltype |
| change_form_stat | change_form_stat |
| example of cutsite | cutsite |
| example of data | data |
| example_data | example_data |
| FindIndel | FindIndel |
| IndelForm | IndelForm |
| IndelIdents | IndelIdents |
| IndelPlot | IndelPlot |
| PlotTree | PlotTree |
| ReadCutsite | ReadCutsite |
| ReadFasta | ReadFasta |
| example of ref | ref |
| example of scarform | scarform |
| example of scarinfo | scarinfo |
| example of scarref | scarref |
| example of scarref_all | scarref_all |
| example of tag | tag |
| TagDist | TagDist |
| TagProcess | TagProcess |
| example of treeinfo | treeinfo |
