Package: copyseparator 1.2.0

copyseparator: Assembling Long Gene Copies from Short Read Data

Assembles two or more gene copies from short-read Next-Generation Sequencing data. Works best when there are only two gene copies and read length >=250 base pairs. High and relatively even coverage are important.

Authors:Lei Yang

copyseparator_1.2.0.tar.gz
copyseparator_1.2.0.zip(r-4.5)copyseparator_1.2.0.zip(r-4.4)copyseparator_1.2.0.zip(r-4.3)
copyseparator_1.2.0.tgz(r-4.4-any)copyseparator_1.2.0.tgz(r-4.3-any)
copyseparator_1.2.0.tar.gz(r-4.5-noble)copyseparator_1.2.0.tar.gz(r-4.4-noble)
copyseparator_1.2.0.tgz(r-4.4-emscripten)copyseparator_1.2.0.tgz(r-4.3-emscripten)
copyseparator.pdf |copyseparator.html
copyseparator/json (API)
NEWS

# Install 'copyseparator' in R:
install.packages('copyseparator', repos = c('https://leiyang-fish.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/leiyang-fish/copyseparator/issues

On CRAN:

3.70 score 2 scripts 199 downloads 6 exports 48 dependencies

Last updated 4 months agofrom:8046ae6369. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 30 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 30 2024
R-4.4-macWARNINGOct 30 2024
R-4.3-winWARNINGOct 30 2024
R-4.3-macWARNINGOct 30 2024

Exports:copy_assemblecopy_detectcopy_separatecopy_validatesep_assemsubset_downsize

Dependencies:ade4apeaskpassaudiobeeprBiocGenericsBiostringsclicodetoolscrayoncurlDBIDECIPHERdigestdoParallelforeachGenomeInfoDbGenomeInfoDbDatagluehttrIRangesiteratorsjsonlitekmerlatticelifecyclemagrittrMASSmimenlmeopensslphylogrampixmapR6RcppRcppArmadillorlangS4VectorssegmentedseqinrspstringistringrsysUCSC.utilsvctrsXVectorzlibbioc

Usage_of_copyseparator

Rendered fromUsage_of_copyseparator.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-11-23
Started: 2022-11-23

Readme and manuals

Help Manual

Help pageTopics
copy_assemblecopy_assemble
copy_detectcopy_detect
copy_separatecopy_separate
copy_validatecopy_validate
sep_assemsep_assem
subset_downsizesubset_downsize