Scripture specifications


Unique identifier OMICS_01265
Name Scripture
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Mitchell Guttman <>
  • person_outline Manuel Garber <>
  • person_outline Aviv Regev <>

Scripture article

Scripture citations

PMCID: 4877582

[…] individual libraries were converted to the fastq format. sequence reads were aligned to the human genome (hg19) with tophat2 and the resulting alignment files were reconstructed with cufflinks50 and scripture51. for mrna analyses, the refseq database (build 37.3) was chosen as the annotation references. for lncrna analyses, the gencode v19 database was chosen as the annotation references. […]

PMCID: 3905897

[…] revealed a growing body of putative lncrnas (28,54,55,67–69). it has been established that the expression of lncrnas is strongly associated with vertebrate development (54,55,67,69). cufflinks and scripture are two earlier pioneering tools that can assemble and quantify transcriptome-wide coding and non-coding transcripts based directly on rna-seq data (67,70). other programs or pipelines […]

Scripture institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
Scripture funding source(s)
Supported by a Burroughs Wellcome Fund Career Award at the Scientific Interface, an NIH PIONEER award, an NHGRI R01, and the Howard Hughes Medical Institute, and NHGRI and the Broad Institute of MIT and Harvard.

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