Package: seqmagick 0.1.7
Guangchuang Yu
seqmagick: Sequence Manipulation Utilities
Supports reading and writing sequences for different formats (currently interleaved and sequential formats for 'FASTA' and 'PHYLIP'), file conversion, and manipulation (e.g. filter sequences that contain specify pattern, export consensus sequence from an alignment).
Authors:
seqmagick_0.1.7.tar.gz
seqmagick_0.1.7.zip(r-4.5)seqmagick_0.1.7.zip(r-4.4)seqmagick_0.1.7.zip(r-4.3)
seqmagick_0.1.7.tgz(r-4.4-any)seqmagick_0.1.7.tgz(r-4.3-any)
seqmagick_0.1.7.tar.gz(r-4.5-noble)seqmagick_0.1.7.tar.gz(r-4.4-noble)
seqmagick_0.1.7.tgz(r-4.4-emscripten)seqmagick_0.1.7.tgz(r-4.3-emscripten)
seqmagick.pdf |seqmagick.html✨
seqmagick/json (API)
NEWS
| # Install 'seqmagick' in R: |
| install.packages('seqmagick', repos = c('https://yulab-smu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yulab-smu/seqmagick/issues
Last updated 10 months agofrom:71ead12273. Checks:OK: 5 WARNING: 1 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 03 2024 |
| R-4.5-win | OK | Nov 03 2024 |
| R-4.5-linux | WARNING | Nov 03 2024 |
| R-4.4-win | OK | Nov 03 2024 |
| R-4.4-mac | OK | Nov 03 2024 |
| R-4.3-win | OK | Nov 03 2024 |
| R-4.3-mac | NOTE | Nov 03 2024 |
Exports:bam2DNAStringSetbam2DNAStringSet2bs_alnbs_consensusbs_filterbs_hammingbs_renameclw_readconsensusdownload_genbankfa_combinefa_filterfa_readfa_renamefa_to_interleavedfa_to_sequentialfa_writefas2phygb_readget_idmega_readphy_readphy_writephy2fasrenameTXTreplaceInsideseqlensth_read
Dependencies:askpassBiocGenericsBiostringsclicrayoncurldigestfsgenericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemagrittrmimeopensslR6rlangS4VectorssysUCSC.utilsXVectoryulab.utilszlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| bam2DNAStringSet | bam2DNAStringSet |
| bam2DNAStringSet2 | bam2DNAStringSet2 |
| bs_aln | bs_aln |
| bs_filter | bs_filter |
| bs_hamming | bs_hamming |
| bs_rename | bs_rename |
| consensus | bs_consensus consensus |
| download_genbank | download_genbank |
| fa_combine | fa_combine |
| fa_filter | fa_filter |
| fa_rename | fa_rename |
| fa_to_interleaved | fa_to_interleaved fa_to_sequential |
| fa_write | fa_write |
| fas2phy | fas2phy |
| gb_read | gb_read |
| get_id | get_id |
| read sequence alignment file | clw_read fa_read mega_read sth_read |
| phy_read | phy_read |
| phy_write | phy_write |
| phy2fas | phy2fas |
| renameTXT | renameTXT |
| replaceInside | replaceInside |
| seqlen | seqlen |
