Package: TAPseq 1.19.0

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_1.19.0.tar.gz
TAPseq_1.19.0.zip(r-4.5)TAPseq_1.19.0.zip(r-4.4)TAPseq_1.19.0.zip(r-4.3)
TAPseq_1.19.0.tgz(r-4.4-any)TAPseq_1.19.0.tgz(r-4.3-any)
TAPseq_1.19.0.tar.gz(r-4.5-noble)TAPseq_1.19.0.tar.gz(r-4.4-noble)
TAPseq_1.19.0.tgz(r-4.4-emscripten)TAPseq_1.19.0.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'))

Peer review:

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

Datasets:

On BioConductor:TAPseq-1.19.0(bioc 3.21)TAPseq-1.18.0(bioc 3.20)

singlecellsequencingtechnologycrisprpooledscreens

5.56 score 4 stars 9 scripts 194 downloads 42 exports 82 dependencies

Last updated 25 days agofrom:e6e4d9cd86. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 18 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macWARNINGNov 18 2024

Exports:beads_oligobeads_oligo<-blastPrimerscheckPrimerscreateBLASTDbcreateIORecordcreatePrimerTrackdesignPrimersexportPrimerTrackgetTxsSeqinferPolyASitesmin_primer_regionmin_primer_region<-pcr_productspickPrimersplotTargetGenesprimer_max_tmprimer_max_tm<-primer_min_tmprimer_min_tm<-primer_num_returnprimer_num_return<-primer_opt_tmprimer_opt_tm<-primerDataFrameproduct_size_rangeproduct_size_range<-reverse_primerreverse_primer<-selectTargetGenessequence_idsequence_id<-sequence_templatetapseq_primersTAPseqInputtarget_annottarget_annot<-target_sequencetarget_sequence<-truncateTxsPolyATsIOTsIOList

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfansifastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngpurrrR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLXVectoryamlzlibbioc

Select target genes for TAP-seq

Andreas Gschwind

Rendered fromtapseq_target_genes.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

TAP-seq primer design workflow

Andreas Gschwind

Rendered fromtapseq_primer_design.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Accessors for TsIO objectsaccessors 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 databone_marrow_genex
Check primers for complementaritycheckPrimers checkPrimers,TsIO-method checkPrimers,TsIOList-method
Chromosome 11 geneschr11_genes
Chromosome 11 polyA siteschr11_polyA_sites
Chromosome 11 primerschr11_primers
Chromosome 11 truncated transcriptschr11_truncated_txs
Chromosome 11 truncated transcript sequenceschr11_truncated_txs_seq
Create boulder IO recordcreateIORecord createIORecord,TsIO-method createIORecord,TsIOList-method
Design primersdesignPrimers designPrimers,TsIO-method designPrimers,TsIOList-method
Estimate primer off-targets using BLASTblastPrimers blastPrimers,TsIO-method blastPrimers,TsIOList-method createBLASTDb estimateOffTargets
Export TAP-seq primerscreatePrimerTrack createPrimerTrack,TsIO-method createPrimerTrack,TsIOList-method exportPrimers exportPrimerTrack primerDataFrame primerDataFrame,TsIO-method primerDataFrame,TsIOList-method
Get transcript sequencesgetTxsSeq getTxsSeq,GRanges-method getTxsSeq,GRangesList-method
Infer polyA sites from droplet sequencing datainferPolyASites
Pick best TAP-seq primerspickPrimers pickPrimers,TsIO-method pickPrimers,TsIOList-method
Select target genesplotTargetGenes selectTargetGenes
TAPseq: R-package to design primers for TAP-seqTAPseq
Create TAPseq input from target sequencesTAPseqInput
Truncate transcripts at polyA sitestruncateTxsPolyA truncateTxsPolyA,GRanges-method truncateTxsPolyA,GRangesList-method
TsIO classbeads_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 classpcr_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