SuperTranscript statistics

info info

Citations per year

info

Popular tool citations

chevron_left Transcriptome viewers chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

SuperTranscript specifications

Information


Unique identifier OMICS_12974
Name SuperTranscript
Alternative name Lace
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Group of transcripts, de novo contigs, reference sequence, long reads (or a mixture of all the above)
Input format FASTA, TXT
Output format FASTA, GFF, PSL, PDF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, R
Computer skills Advanced
Stability Stable
Requirements
Pandas, Networkx, Numpy, Matplotlib
Maintained Yes

Download


download.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Alicia Oshlack

Additional information


https://github.com/Oshlack/Lace

Publication for SuperTranscript

SuperTranscript citations

 (6)
library_books

Genome Informatics 2016

2017
Genome Biol
PMCID: 5240446
PMID: 28093077
DOI: 10.1186/s13059-016-1135-5

[…] a method for efficiently detecting de novo mutation using k-mer counting instead of reference-guided alignment. alicia oshlack (murdoch childrens research institute, australia) presented the supertranscript model for enhancing transcriptome visualization (https://github.com/oshlack/lace/wiki). jouni sirén (wellcome trust sanger institute, uk) presented a method to index population […]

library_books

Transcriptomic Analysis of Cadmium Stress Response in the Heavy Metal Hyperaccumulator Sedum alfredii Hance

2013
PLoS One
PMCID: 3670878
PMID: 23755133
DOI: 10.1371/journal.pone.0064643

[…] differences between treatments . for qrt-pcr analysis, total rna from three biological replicates was isolated (qiagen, germany) from shoots of he and nhe, and reverse transcribed using the supertranscript iii rt kit (invitrogen, usa) according to the manufacturer’s instructions. for primer design (), blast searches were conducted against the arabidopsis nucleotide database with s. […]

library_books

Germline SDHx variants modify breast and thyroid cancer risks in Cowden and Cowden like syndrome via FAD/NAD dependant destabilization of p53

2011
Hum Mol Genet
PMCID: 3276278
PMID: 21979946
DOI: 10.1093/hmg/ddr459

[…] the manufacturer's protocol, and subsequently treated with dnase i (invitrogen, carlsbad, ca, usa). dnase-treated total rna from each lcl was reverse-transcribed into cdna using random primers and supertranscript™ iii reverse transcriptase (invitrogen), as specified by the manufacturer. pcr was performed using sybr green pcr master mix and run on 7500 real time pcr machine (applied biosystem, […]

library_books

A tissue specific landscape of sense/antisense transcription in the mouse intestine

2011
BMC Genomics
PMCID: 3125268
PMID: 21663663
DOI: 10.1186/1471-2164-12-305

[…] included data on transcript isoforms was removed from the refseq table by allowing gene symbols only once within the refseq table. transcripts sharing a gene symbol were artificially fused to a 'supertranscript', so that expression of either isoform led to detection of the corresponding gene symbol. reads were randomly drawn and removed from the entirety of matched reads. drawn reads located […]

library_books

Naturally occurring germline and tumor associated mutations within the ATP binding motifs of PTEN lead to oxidative damage of DNA associated with decreased nuclear p53

2010
Hum Mol Genet
PMCID: 3000677
PMID: 20926450
DOI: 10.1093/hmg/ddq434

[…] valencia, ca, usa) according to the manufacturer's protocol, and subsequently treated with dnase i (invitrogen). dnase-treated total rna was reverse-transcribed into cdna using random primers and supertranscript™ iii reverse transcriptase (invitrogen), as specified by the manufacturer. polymerase chain reaction was performed using sybr green pcr master mix and run on 7500 real time pcr […]

library_books

Expressions of ECE CYC2 clade genes relating to abortion of both dorsal and ventral stamens in Opithandra (Gesneriaceae)

2009
BMC Evol Biol
PMCID: 2763874
PMID: 19811633
DOI: 10.1186/1471-2148-9-244

[…] from the floral buds of o. dinghushanensis using the plant rna purification reagent (invitrogen) according to the manufacture's protocol. first-strand cdnas were synthesized from total rna with the supertranscript™ iii rnase h- reverse transcriptase (invitrogen). to examine the intron/exon structures we isolated and sequenced the corresponding genomic dna of opdcyc and opdcyclind3 genes […]


Want to access the full list of citations?
SuperTranscript institution(s)
Murdoch Childrens Research Institute, Royal Children’s Hospital, Victoria, Australia; School of BioSciences, University of Melbourne, Victoria, Australia
SuperTranscript funding source(s)
This project was funded by an NHMRC Career Development Fellowship APP1051481.

SuperTranscript reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SuperTranscript