Package: MicroSEC 2.1.6
MicroSEC: Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded Samples
Clinical sequencing of tumor is usually performed on formalin-fixed and paraffin-embedded samples and have many sequencing errors. We found that the majority of these errors are detected in chimeric read caused by single-strand DNA with micro-homology. Our filtering pipeline focuses on the uneven distribution of the artifacts in each read and removes such errors in formalin-fixed and paraffin-embedded samples without over-eliminating the true mutations detected in fresh frozen samples.
Authors:
MicroSEC_2.1.6.tar.gz
MicroSEC_2.1.6.zip(r-4.5)MicroSEC_2.1.6.zip(r-4.4)MicroSEC_2.1.6.zip(r-4.3)
MicroSEC_2.1.6.tgz(r-4.4-any)MicroSEC_2.1.6.tgz(r-4.3-any)
MicroSEC_2.1.6.tar.gz(r-4.5-noble)MicroSEC_2.1.6.tar.gz(r-4.4-noble)
MicroSEC_2.1.6.tgz(r-4.4-emscripten)MicroSEC_2.1.6.tgz(r-4.3-emscripten)
MicroSEC.pdf |MicroSEC.html✨
MicroSEC/json (API)
NEWS
| # Install 'MicroSEC' in R: |
| install.packages('MicroSEC', repos = c('https://mano-b.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mano-b/microsec/issues
- exampleBam - An example BAM file.
- exampleMutation - An example mutation file.
- homology_searched - An example sequence information file.
- msec_analyzed - An example mutation file.
- msec_homology_searched - An example mutation file.
- msec_read_checked - An example mutation file.
- msec_summarized - An example mutation file.
- mut_depth_checked - An example sequence information file.
Last updated 1 hours agofrom:6bf8572d34. Checks:OK: 3 NOTE: 2 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 18 2024 |
| R-4.5-win | OK | Sep 18 2024 |
| R-4.5-linux | OK | Sep 18 2024 |
| R-4.4-win | NOTE | Sep 18 2024 |
| R-4.4-mac | ERROR | Sep 18 2024 |
| R-4.3-win | ERROR | Sep 18 2024 |
| R-4.3-mac | NOTE | Sep 18 2024 |
Exports:fun_analysisfun_homologyfun_load_bamfun_load_chr_nofun_load_genomefun_load_mutationfun_read_checkfun_savefun_summary
Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopsclicodetoolscpp11crayoncurldplyrfansiformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelambda.rlifecyclemagrittrmimeopensslpillarpkgconfigR6RhtslibrlangRsamtoolsS4VectorssnowstringistringrsystibbletidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| An example BAM file. | exampleBam |
| An example mutation file. | exampleMutation |
| Analyzing function. | fun_analysis |
| Hairpin-structure sequence check function | fun_hairpin_check |
| Homology check function. | fun_homology |
| BAM file loader | fun_load_bam |
| Chromosome number loading function. | fun_load_chr_no |
| Genome loading function. | fun_load_genome |
| Mutation data file loader | fun_load_mutation |
| Read check function. | fun_read_check |
| Repeat check function. | fun_repeat_check |
| Save function. | fun_save |
| Mutated position search function. | fun_setting |
| Summarizing function. | fun_summary |
| Divide function without 0/0 errors | fun_zero |
| An example sequence information file. | homology_searched |
| An example mutation file. | msec_analyzed |
| An example mutation file. | msec_homology_searched |
| An example mutation file. | msec_read_checked |
| An example mutation file. | msec_summarized |
| An example sequence information file. | mut_depth_checked |
