Package: CellBarcode 1.11.0

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:Wenjie Sun [cre, aut], Anne-Marie Lyne [aut], Leila Perie [aut]

CellBarcode_1.11.0.tar.gz
CellBarcode_1.11.0.zip(r-4.5)CellBarcode_1.11.0.zip(r-4.4)CellBarcode_1.11.0.zip(r-4.3)
CellBarcode_1.11.0.tgz(r-4.4-x86_64)CellBarcode_1.11.0.tgz(r-4.3-x86_64)
CellBarcode_1.11.0.tar.gz(r-4.5-noble)CellBarcode_1.11.0.tar.gz(r-4.4-noble)
CellBarcode_1.11.0.tgz(r-4.4-emscripten)CellBarcode_1.11.0.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'))

Peer review:

Bug tracker:https://github.com/wenjie1991/cellbarcode/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • bc_obj - A dummy BarcodeObj object

On BioConductor:CellBarcode-1.11.0(bioc 3.20)CellBarcode-1.10.0(bioc 3.19)

bioconductor-package

33 exports 1.08 score 92 dependencies

Last updated 2 months agofrom:85eb0aa79c

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.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegridExtragtablehttrhwriterinterpIRangesisobandjpegjsonlitelabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpixmappkgconfigplyrpngpwalignR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackRhtslibrlangRsamtoolsS4ArraysS4VectorsscalessegmentedseqinrShortReadsnowspSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Get barcode from 10X Genomics scRNASeq data

Wenjie Sun

Rendered fromBarcode_in_10X_scRNASeq.Rmdusingknitr::rmarkdownon Jun 17 2024.

Last update: 2024-02-19
Started: 2022-10-10

Analyzing Cellular DNA Barcode with CellBarcode

Wenjie Sun, Anne-Marie Lyne

Rendered fromUMI_VDJ_Barcode.Rmdusingknitr::rmarkdownon Jun 17 2024.

Last update: 2022-10-10
Started: 2021-03-19

Readme and manuals

Help Manual

Help pageTopics
BarcodeObj objectBarcodeObj BarcodeObj-class
Transforms BarcodeObj object into another data typebc_2df bc_2df,BarcodeObj-method bc_2dt bc_2dt,BarcodeObj-method bc_2matrix bc_2matrix,BarcodeObj-method
Finds barcode count cutoff pointbc_auto_cutoff bc_auto_cutoff,BarcodeObj-method
Gets barcode sequencesbc_barcodes bc_barcodes,BarcodeObj-method
Accesses cleanBc slot in the BarcodeObj objectbc_cleanBc bc_cleanBc,BarcodeObj-method
Create a BarcodeObj object from extracted barcodes databc_create_BarcodeObj bc_create_BarcodeObj,data.frame-method bc_create_BarcodeObj,matrix-method
Clean barcodes by editing distancebc_cure_cluster bc_cure_cluster,BarcodeObj-method
Filters barcodes by countsbc_cure_depth bc_cure_depth,BarcodeObj-method
Filters UMI-barcode tag by countsbc_cure_umi bc_cure_umi,BarcodeObj-method
Extract barcode from sequencesbc_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 filebc_extract_sc_fastq
Extract barcode from single-cell sequencing sam filebc_extract_sc_bam bc_extract_sc_sam
Accesses messyBc slot in the BarcodeObj objectbc_messyBc bc_messyBc,BarcodeObj-method
Accesses and sets metadata in BarcodeObj objectbc_meta bc_meta,BarcodeObj-method bc_meta<- bc_meta<-,BarcodeObj-method
Access & update sample names in BarcodeObj & and BarcodeQcSetbc_names bc_names,BarcodeObj-method bc_names,BarcodeQcSet-method bc_names<- bc_names<-,BarcodeObj,character-method bc_names<-,BarcodeQcSet,ANY-method
A dummy BarcodeObj objectbc_obj
Plot for counts distributionbc_plot_count bc_plot_count,BarcodeObj-method
Barcode read count 2D scatter plot of sample combinationbc_plot_mutual bc_plot_mutual,BarcodeObj-method
Barcode read count 2D scatter plot for given pairsbc_plot_pair bc_plot_pair,BarcodeObj-method
Scatter plot of barcode count distribution per samplebc_plot_single bc_plot_single,BarcodeObj-method
Remove low-quality sequencebc_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 qualityBarcodeQc 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 diversitybc_summary_barcode bc_summary_barcode,BarcodeObj-method
Summary barcodeQcSetbc_summary_seqQc bc_summary_seqQc,BarcodeQcSet-method
DNA Barcode Analysis toolkitCellBarcode
Formats BarcodeObj objectformat,BarcodeObj-method
Parse 10X bam fileparse_10x_sam
Sequence clusteringseq_correct
Show BarcodeObj objectshow,BarcodeObj-method show,BarcodeQc-method show,BarcodeQcSet-method
Subset the BarcodeQcSetsubset,BarcodeQcSet-method [,BarcodeQcSet,ANY,ANY,ANY-method