Package: CellBarcode 1.13.1
Wenjie Sun
CellBarcode: Cellular DNA Barcode Analysis toolkit
The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \code{CellBarcode} can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.
Authors:
CellBarcode_1.13.1.tar.gz
CellBarcode_1.13.1.zip(r-4.5)CellBarcode_1.13.1.zip(r-4.4)CellBarcode_1.13.1.zip(r-4.3)
CellBarcode_1.13.1.tgz(r-4.4-x86_64)CellBarcode_1.13.1.tgz(r-4.4-arm64)CellBarcode_1.13.1.tgz(r-4.3-x86_64)CellBarcode_1.13.1.tgz(r-4.3-arm64)
CellBarcode_1.13.1.tar.gz(r-4.5-noble)CellBarcode_1.13.1.tar.gz(r-4.4-noble)
CellBarcode_1.13.1.tgz(r-4.4-emscripten)CellBarcode_1.13.1.tgz(r-4.3-emscripten)
CellBarcode.pdf |CellBarcode.html✨
CellBarcode/json (API)
NEWS
| # Install 'CellBarcode' in R: |
| install.packages('CellBarcode', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wenjie1991/cellbarcode/issues
Pkgdown:https://wenjie1991.github.io
- bc_obj - A dummy BarcodeObj object
On BioConductor:CellBarcode-1.13.0(bioc 3.21)CellBarcode-1.12.0(bioc 3.20)
preprocessingqualitycontrolsequencingcrisprampliconamplicon-sequencingcellular-barcodecpp
Last updated 6 days agofrom:f32bb3345c. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 17 2024 |
| R-4.5-win-x86_64 | NOTE | Dec 17 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 17 2024 |
| R-4.4-win-x86_64 | NOTE | Dec 17 2024 |
| R-4.4-mac-x86_64 | NOTE | Dec 17 2024 |
| R-4.4-mac-aarch64 | NOTE | Dec 17 2024 |
| R-4.3-win-x86_64 | NOTE | Dec 17 2024 |
| R-4.3-mac-x86_64 | NOTE | Dec 17 2024 |
| R-4.3-mac-aarch64 | NOTE | Dec 17 2024 |
Exports:bc_2dfbc_2dtbc_2matrixbc_auto_cutoffbc_barcodesbc_cleanBcbc_create_BarcodeObjbc_cure_clusterbc_cure_depthbc_cure_umibc_extractbc_extract_sc_bambc_extract_sc_fastqbc_extract_sc_sambc_mergebc_messyBcbc_metabc_meta<-bc_namesbc_names<-bc_plot_countbc_plot_mutualbc_plot_pairbc_plot_seqQcbc_plot_singlebc_seq_filterbc_seq_qcbc_splitVDJbc_subsetbc_summary_barcodebc_summary_seqQcformatshow
Dependencies:abindade4askpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsCkmeans.1d.dpclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydeldireggfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegridExtragtablehttrhwriterinterpIRangesisobandjpegjsonlitelabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpixmappkgconfigplyrpngpwalignR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackRhtslibrlangRsamtoolsS4ArraysS4VectorsscalessegmentedseqinrShortReadsnowspSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Get barcode from 10X Genomics scRNASeq data
Rendered fromBarcode_in_10X_scRNASeq.Rmdusingknitr::rmarkdownon Dec 17 2024.Last update: 2024-02-19
Started: 2022-10-10
Analyzing Cellular DNA Barcode with CellBarcode
Rendered fromUMI_VDJ_Barcode.Rmdusingknitr::rmarkdownon Dec 17 2024.Last update: 2022-10-10
Started: 2021-03-19
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| BarcodeObj object | BarcodeObj BarcodeObj-class |
| Transforms BarcodeObj object into another data type | bc_2df bc_2df,BarcodeObj-method bc_2dt bc_2dt,BarcodeObj-method bc_2matrix bc_2matrix,BarcodeObj-method |
| Finds barcode count cutoff point | bc_auto_cutoff bc_auto_cutoff,BarcodeObj-method |
| Gets barcode sequences | bc_barcodes bc_barcodes,BarcodeObj-method |
| Accesses cleanBc slot in the BarcodeObj object | bc_cleanBc bc_cleanBc,BarcodeObj-method |
| Create a BarcodeObj object from extracted barcodes data | bc_create_BarcodeObj bc_create_BarcodeObj,data.frame-method bc_create_BarcodeObj,matrix-method |
| Clean barcodes by editing distance | bc_cure_cluster bc_cure_cluster,BarcodeObj-method |
| Filters barcodes by counts | bc_cure_depth bc_cure_depth,BarcodeObj-method |
| Filters UMI-barcode tag by counts | bc_cure_umi bc_cure_umi,BarcodeObj-method |
| Extract barcode from sequences | bc_extract bc_extract,character-method bc_extract,data.frame-method bc_extract,DNAStringSet-method bc_extract,integer-method bc_extract,list-method bc_extract,ShortReadQ-method |
| Extract barcode from single-cell sequencing fastq file | bc_extract_sc_fastq |
| Extract barcode from single-cell sequencing sam file | bc_extract_sc_bam bc_extract_sc_sam |
| Accesses messyBc slot in the BarcodeObj object | bc_messyBc bc_messyBc,BarcodeObj-method |
| Accesses and sets metadata in BarcodeObj object | bc_meta bc_meta,BarcodeObj-method bc_meta<- bc_meta<-,BarcodeObj-method |
| Access & update sample names in BarcodeObj & and BarcodeQcSet | bc_names bc_names,BarcodeObj-method bc_names,BarcodeQcSet-method bc_names<- bc_names<-,BarcodeObj,character-method bc_names<-,BarcodeQcSet,ANY-method |
| A dummy BarcodeObj object | bc_obj |
| Plot for counts distribution | bc_plot_count bc_plot_count,BarcodeObj-method |
| Barcode read count 2D scatter plot of sample combination | bc_plot_mutual bc_plot_mutual,BarcodeObj-method |
| Barcode read count 2D scatter plot for given pairs | bc_plot_pair bc_plot_pair,BarcodeObj-method |
| Scatter plot of barcode count distribution per sample | bc_plot_single bc_plot_single,BarcodeObj-method |
| Remove low-quality sequence | bc_seq_filter bc_seq_filter,character-method bc_seq_filter,data.frame-method bc_seq_filter,DNAStringSet-method bc_seq_filter,integer-method bc_seq_filter,list-method bc_seq_filter,ShortReadQ-method |
| Evaluates sequences quality | BarcodeQc BarcodeQc-class BarcodeQcSet BarcodeQcSet-class bc_plot_seqQc bc_plot_seqQc,BarcodeQc-method bc_plot_seqQc,BarcodeQcSet-method bc_seq_qc bc_seq_qc,character-method bc_seq_qc,data.frame-method bc_seq_qc,DNAStringSet-method bc_seq_qc,integer-method bc_seq_qc,list-method bc_seq_qc,ShortReadQ-method |
| Parse VDJ recombination (experimental) | bc_splitVDJ |
| Manages barcodes and samples in a BarcodeObj object | *.BarcodeObj +.BarcodeObj -.BarcodeObj bc_merge bc_merge,BarcodeObj,BarcodeObj-method bc_subset bc_subset,BarcodeObj-method |
| Summary and evaluate barcode diversity | bc_summary_barcode bc_summary_barcode,BarcodeObj-method |
| Summary barcodeQcSet | bc_summary_seqQc bc_summary_seqQc,BarcodeQcSet-method |
| DNA Barcode Analysis toolkit | CellBarcode-package CellBarcode |
| Formats BarcodeObj object | format,BarcodeObj-method |
| Parse 10X bam file | parse_10x_sam |
| Sequence clustering | seq_correct |
| Show BarcodeObj object | show,BarcodeObj-method show,BarcodeQc-method show,BarcodeQcSet-method |
| Subset the BarcodeQcSet | subset,BarcodeQcSet-method [,BarcodeQcSet,ANY,ANY,ANY-method |
