Package: TAPseq 1.17.0

Andreas R. Gschwind

TAPseq: Targeted scRNA-seq primer design for TAP-seq

Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using Primer3. Potential off-targets can be estimated with BLAST. Requires working installations of Primer3 and BLASTn.

Authors:Andreas R. Gschwind [aut, cre], Lars Velten [aut], Lars M. Steinmetz [aut]

TAPseq_1.17.0.tar.gz
TAPseq_1.17.0.zip(r-4.5)TAPseq_1.17.0.zip(r-4.4)TAPseq_1.17.0.zip(r-4.3)
TAPseq_1.17.0.tgz(r-4.4-any)TAPseq_1.17.0.tgz(r-4.3-any)
TAPseq_1.17.0.tar.gz(r-4.5-noble)TAPseq_1.17.0.tar.gz(r-4.4-noble)
TAPseq_1.17.0.tgz(r-4.4-emscripten)TAPseq_1.17.0.tgz(r-4.3-emscripten)
TAPseq.pdf |TAPseq.html✨
TAPseq/json (API)
NEWS

# Install 'TAPseq' in R:

install.packages('TAPseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/argschwind/tapseq/issues

Datasets:

bone_marrow_genex - Mouse bone marrow 10x data
chr11_genes - Chromosome 11 genes
chr11_polyA_sites - Chromosome 11 polyA sites
chr11_primers - Chromosome 11 primers
chr11_truncated_txs - Chromosome 11 truncated transcripts
chr11_truncated_txs_seq - Chromosome 11 truncated transcript sequences

On BioConductor:TAPseq-1.17.0(bioc 3.20)TAPseq-1.16.0(bioc 3.19)

bioconductor-package

42 exports 0.82 score 82 dependencies

Last updated 2 months agofrom:9e5cbf0d87

Exports:beads_oligo beads_oligo<-blastPrimers checkPrimers createBLASTDb createIORecord createPrimerTrack designPrimers exportPrimerTrack getTxsSeq inferPolyASites min_primer_region min_primer_region<-pcr_products pickPrimers plotTargetGenes primer_max_tm primer_max_tm<-primer_min_tm primer_min_tm<-primer_num_return primer_num_return<-primer_opt_tm primer_opt_tm<-primerDataFrame product_size_range product_size_range<-reverse_primer reverse_primer<-selectTargetGenes sequence_id sequence_id<-sequence_template tapseq_primers TAPseqInput target_annot target_annot<-target_sequence target_sequence<-truncateTxsPolyA TsIO TsIOList

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl DBI DelayedArray dplyr fansi fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png purrr R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XML XVector yaml zlibbioc

Select target genes for TAP-seq

Andreas Gschwind

Rendered fromtapseq_target_genes.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2021-10-18
Started: 2020-02-21

TAP-seq primer design workflow

Andreas Gschwind

Rendered fromtapseq_primer_design.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2023-11-07
Started: 2020-01-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Accessors for TsIO objects	accessors beads_oligo beads_oligo<- min_primer_region min_primer_region<- pcr_products primer_max_tm primer_max_tm<- primer_min_tm primer_min_tm<- primer_num_return primer_num_return<- primer_opt_tm primer_opt_tm<- product_size_range product_size_range<- reverse_primer reverse_primer<- sequence_id sequence_id<- sequence_template tapseq_primers target_annot target_annot<- target_sequence target_sequence<-
Mouse bone marrow 10x data	bone_marrow_genex
Check primers for complementarity	checkPrimers checkPrimers,TsIO-method checkPrimers,TsIOList-method
Chromosome 11 genes	chr11_genes
Chromosome 11 polyA sites	chr11_polyA_sites
Chromosome 11 primers	chr11_primers
Chromosome 11 truncated transcripts	chr11_truncated_txs
Chromosome 11 truncated transcript sequences	chr11_truncated_txs_seq
Create boulder IO record	createIORecord createIORecord,TsIO-method createIORecord,TsIOList-method
Design primers	designPrimers designPrimers,TsIO-method designPrimers,TsIOList-method
Estimate primer off-targets using BLAST	blastPrimers blastPrimers,TsIO-method blastPrimers,TsIOList-method createBLASTDb estimateOffTargets
Export TAP-seq primers	createPrimerTrack createPrimerTrack,TsIO-method createPrimerTrack,TsIOList-method exportPrimers exportPrimerTrack primerDataFrame primerDataFrame,TsIO-method primerDataFrame,TsIOList-method
Get transcript sequences	getTxsSeq getTxsSeq,GRanges-method getTxsSeq,GRangesList-method
Infer polyA sites from droplet sequencing data	inferPolyASites
Pick best TAP-seq primers	pickPrimers pickPrimers,TsIO-method pickPrimers,TsIOList-method
Select target genes	plotTargetGenes selectTargetGenes
TAPseq: R-package to design primers for TAP-seq	TAPseq
Create TAPseq input from target sequences	TAPseqInput
Truncate transcripts at polyA sites	truncateTxsPolyA truncateTxsPolyA,GRanges-method truncateTxsPolyA,GRangesList-method
TsIO class	beads_oligo,TsIO-method beads_oligo<-,TsIO-method min_primer_region,TsIO-method min_primer_region<-,TsIO-method pcr_products,TsIO-method primer_max_tm,TsIO-method primer_max_tm<-,TsIO-method primer_min_tm,TsIO-method primer_min_tm<-,TsIO-method primer_num_return,TsIO-method primer_num_return<-,TsIO-method primer_opt_tm,TsIO-method primer_opt_tm<-,TsIO-method product_size_range,TsIO-method product_size_range<-,TsIO-method reverse_primer,TsIO-method reverse_primer<-,TsIO-method sequence_id,TsIO-method sequence_id<-,TsIO-method sequence_template,TsIO-method tapseq_primers,TsIO-method target_annot,TsIO-method target_annot<-,TsIO-method target_sequence,TsIO-method target_sequence<-,TsIO-method TsIO TsIO-class
TsIOList class	pcr_products,TsIOList-method sequence_id,TsIOList-method sequence_template,TsIOList-method tapseq_primers,TsIOList-method target_annot,TsIOList-method target_sequence,TsIOList-method TsIOList TsIOList-class