TAPDANCE statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

TAPDANCE specifications

Information


Unique identifier OMICS_22326
Name TAPDANCE
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A set of 4 files including a sequence file produced by the high-throughput sequencing machine, a barcode sequences mapped to library names, a set of metadata characteristics describing the sets of libraries for CISs analyses and a list of chromosomes to potentially exclude from the analysis.
Operating system Unix/Linux
Programming languages Perl, R
Computer skills Advanced
Stability Stable
Requirements
Bowtie, PERL DBI
Maintained Yes

Download


download.png

Versioning


No version available

Maintainer


  • person_outline Aaron Sarver

Additional information


https://sourceforge.net/p/tapdancebio/wiki/Home/

Publication for TAPDANCE

TAPDANCE citations

 (6)
call_split

Modulation of the functional association between the HIV 1 intasome and the nucleosome by histone amino terminal tails

2017
Retrovirology
PMCID: 5704366
PMID: 29179726
DOI: 10.1186/s12977-017-0378-x
call_split See protocol

[…] er followed by LTR sequences at the tip of the LTR. The rest of the reads were quality-trimmed as soon as 2 out of 5 bases had quality scores less than a Phred score of 20. We used bowtie [] with the TAPDANCE tool [] to map the reads to the hg19 human genome assembly in cycles with decreasing read length of 60, 55, 50, 45, 40, 35 allowing 3, 3, 3, 2, 1, 0 mismatches, respectively, with the followi […]

library_books

PD 1 is a haploinsufficient suppressor of T cell lymphomagenesis

2017
Nature
PMCID: 5821214
PMID: 29143824
DOI: 10.1038/nature24649

[…] re (NES), false discovery rate (FDR) and p values for the GSEA were calculated with BubbleGUM. The p-values for the common integration sites (CISs) of the PB transposon cassettes were calculated with TAPDANCE; the p-values of “insertions” were used for CIS ranking. The upper tail of the probability density function in was calculated based on the Poisson rate parameter λ derived from TAPDANCE and […]

library_books

Sleeping Beauty transposon screen identifies signaling modules that cooperate with STAT5 activation to induce B cell acute lymphoblastic leukemia

2015
Oncogene
PMCID: 4846597
PMID: 26500062
DOI: 10.1038/onc.2015.405

[…] Common Insertion Sites (CISs) that cooperate with STAT5 to initiate transformation we used a PCR-based approach to amplify T2/Onc insertion sites followed by high throughput sequencing. We used both TAPDANCE and gene-centric (gCIS) analyses to find CIS genetic loci in 65 of our leukemias., The high confidence CIS identified by the TAPDANCE analysis included ten annotated genes and two regions of […]

library_books

The utility of transposon mutagenesis for cancer studies in the era of genome editing

2015
Genome Biol
PMCID: 4612416
PMID: 26481584
DOI: 10.1186/s13059-015-0794-y

[…] uced mutagenesis data, a method that has also been applied to TMIM screens []. In addition, the Poisson regression insertion model (PRIM) [] has been used to identify co-occurring gene pairs, and the TAPDANCE algorithm can generate the association of independent CISs by using a Fisher’s exact test []. […]

call_split

Genetic Signature of Histiocytic Sarcoma Revealed by a Sleeping Beauty Transposon Genetic Screen in Mice

2014
PLoS One
PMCID: 4020815
PMID: 24827933
DOI: 10.1371/journal.pone.0097280
call_split See protocol

[…] ble upon request). PCR amplicons were subjected to sequencing using the Illumina HiSeq 2000 platform following manufacturer's protocol.Sequences were mapped to the mouse genome using BOWTIE using the TAPDANCE bioinformatics pipeline. TAPDANCE identifies CISs based on analysis of varying genomic window sizes, tested for significance using the Poisson distribution (p<0.05) utilizing a Bonferroni cor […]

library_books

Forward genetic screen for malignant peripheral nerve sheath tumor formation identifies new genes and genetic pathways driving tumorigenesis

2013
Nat Genet
PMCID: 3695033
PMID: 23685747
DOI: 10.1038/ng.2641

[…] DNA isolated from SB-derived neurofibromas and grade 3 PNSTs underwent linker-mediated PCR to amplify transposon-genomic DNA junctions and were sequenced as previously described. Identification of TAPDANCE CISs and gene centric CISs from sequenced transposon-genomic DNA PCR products was performed as previously described,. The local-hopping phenomenon of T2/Onc was accounted for by excluding chr […]

Citations

Looking to check out a full list of citations?

TAPDANCE institution(s)
Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA; Obstetrics, Gynecology & Women's Health and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Department of Genetics, Cell Biology and Development and Pediatrics Masonic Cancer Center University of Minnesota, Minneapolis, MN, USA

TAPDANCE reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review TAPDANCE