Introduction | Installation | Creation of SNV profiles | Create individual profiles | Variant filtration | Create multiple profiles | Create COSMIC profiles | Working with profiles on disk | Comparing SNV profiles | Comparing full profiles | Comparing to COSMIC profiles | Evaluating binary comparisons | Similarity and global statistics | Evaluation of SNV impacts | Evaluation of specific chromosomes, regions, genes and transcripts | Evaluating multiple comparisons | Performing multiple profile comparisons | Visualising multiple comparisons | Citation | Session info | References
Package: seqCAT 1.35.0
Erik Fasterius
seqCAT: High Throughput Sequencing Cell Authentication Toolkit
The seqCAT package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and validate the source, function and characteristics of biological samples used in scientific endeavours.
Authors:
seqCAT_1.35.0.tar.gz
seqCAT_1.35.0.zip(r-4.7)seqCAT_1.35.0.zip(r-4.6)seqCAT_1.35.0.zip(r-4.5)
seqCAT_1.35.0.tgz(r-4.6-any)seqCAT_1.35.0.tgz(r-4.5-any)
seqCAT_1.35.0.tar.gz(r-4.7-any)seqCAT_1.35.0.tar.gz(r-4.6-any)
seqCAT_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
seqCAT/json (API)
| # Install 'seqCAT' in R: |
| install.packages('seqCAT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- test_comparison - Overlapping and compared SNVs
- test_profile_1 - SNV profile 1
- test_profile_2 - SNV profile 2
- test_profile_3 - SNV profile 3
- test_similarities - Collated similarities object
- test_variant_list - Modified variant list object
On BioConductor:seqCAT-1.35.0(bioc 3.24)seqCAT-1.34.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
coveragegenomicvariationsequencingvariantannotation
Last updated from:edfcad580e. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 202 | ||
| linux-devel-x86_64 | NOTE | 406 | ||
| source / vignettes | OK | 305 | ||
| linux-release-x86_64 | NOTE | 452 | ||
| macos-release-arm64 | NOTE | 217 | ||
| macos-oldrel-arm64 | NOTE | 204 | ||
| windows-devel | NOTE | 316 | ||
| windows-release | NOTE | 310 | ||
| windows-oldrel | NOTE | 296 | ||
| wasm-release | OK | 168 |
Exports:calculate_similaritycompare_manycompare_profilescreate_profilecreate_profilesfilter_duplicatesfilter_variantslist_cosmiclist_variantsplot_heatmapplot_impactsplot_variant_listread_cosmicread_profileread_profileswrite_profilewrite_profiles
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SNV profile similarity calculations | calculate_similarity |
| Comparisons of many SNV profiles | compare_many |
| Binary SNV profile comparisons | compare_profiles |
| SNV profile creation | create_profile |
| SNV profile creation | create_profiles |
| Variant de-duplication | filter_duplicates |
| Variant filtering | filter_variants |
| List COSMIC sample names | list_cosmic |
| List known variants | list_variants |
| Plot similarity heatmap | plot_heatmap |
| Plot SNV impact distribution | plot_impacts |
| Plot known variants list | plot_variant_list |
| Read COSMIC data | read_cosmic |
| Read SNV profile | read_profile |
| Read SNV profiles | read_profiles |
| seqCAT: High Throughput Sequencing Cell Authentication Toolkit | seqCAT-package seqCAT |
| Overlapping and compared SNVs | test_comparison |
| SNV profile 1 | test_profile_1 |
| SNV profile 2 | test_profile_2 |
| SNV profile 3 | test_profile_3 |
| Collated similarities object | test_similarities |
| Modified variant list object | test_variant_list |
| Write SNV profile | write_profile |
| Write SNV profiles | write_profiles |
