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Information


Unique identifier OMICS_19571
Name INSPEcT
Alternative name INference of Synthesis Processing and dEgradation rates in Time-course analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.10.0
Stability Stable
Requirements
methods, BiocGenerics, Biobase, IRanges, GenomicRanges, Rsamtools, S4Vectors, BiocStyle, GenomicAlignments, BiocParallel, GenomicFeatures, knitr, preprocessCore, R(>=3.2), TxDb.Mmusculus.UCSC.mm9.knownGene, deSolve, pROC, compiler, rootSolve
Maintained Yes

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Documentation


Maintainer


  • person_outline Mattia Pelizzola

Publication for INference of Synthesis Processing and dEgradation rates in Time-course analysis

INSPEcT citations

 (9)
library_books

Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation Induced Bystander Effects (RIBE)

2017
PMCID: 5742808
PMID: 29186820
DOI: 10.3390/cancers9120160

[…] cribed in detail in the limma user’s guide (Section 17.4) []. In parallel, exploratory analysis methodologies, such as unsupervised clustering, were applied to assess any quality problems and also to inspect putative batch effects regarding the experimental design. Finally, to measure the global expression alteration patterns between either bystander versus control or irradiated versus control sam […]

library_books

Post transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq

2017
Nat Commun
PMCID: 5662751
PMID: 29084942
DOI: 10.1038/s41467-017-01126-x

[…] Therefore, these data support the hypothesis that Sfpq plays a role in regulating miRNA silencing on specific binding sites, which globally impact miRNA-dependent gene expression programs.To further inspect the direct role of Sfpq in controlling miRNA targeting in cells, we focused on a particular known let-7a target—the oncogene Lin28A, also known as Lin-28 homolog A, which regulates the self-re […]

library_books

m6A mRNA methylation controls T cell homeostasis by targeting IL 7/STAT5/SOCS pathway

2017
Nature
PMCID: 5729908
PMID: 28792938
DOI: 10.1038/nature23450

[…] ded to the UCSC genome browser. The scale was normalized using exogenous S. pombe RNA added prior to library preparation.Transcript abundance, synthesis and degradation rates were estimated using the INSPEcT package in R . Spearman correlation between samples were visualized using the corrplot package. Transcripts with significant time-dependent changes were determined and clustered using the maSi […]

library_books

CyTOF workflow: differential discovery in high throughput high dimensional cytometry datasets

2017
F1000Res
PMCID: 5473464
PMID: 28663787
DOI: 10.5256/f1000research.12553.r23055

[…] similar cell populations are present in all replicates, which can help in identifying outlying samples. Optionally, stratification can be done by condition (see ). With such a spot-check plot, we can inspect whether differences in cell abundance are strong between conditions, and we can identify distinguishing clusters. dr $ sample_id <- sample_ids[tsne_inds] mm <- match (dr $ sample_id, md $ sam […]

library_books

Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions

2016
Front Genet
PMCID: 4858535
PMID: 27200084
DOI: 10.3389/fgene.2016.00075

[…] ute and differential expression quantification for RNA-Seq, (iii) integrative analysis of nascent and total RNA-seq data, thus quantifying mRNA synthesis, processing and degradation rates through the INSPEcT Bioconductor package that we recently developed (), (iv) identification of DHS regions and digital footprints in DNase-Seq data, (v) determination of absolute and relative methylation levels a […]

library_books

Design, measurement and processing of region specific DNA methylation assays: the mass spectrometry based method EpiTYPER

2015
Front Genet
PMCID: 4585020
PMID: 26442105
DOI: 10.3389/fgene.2015.00287

[…] After the measurement on the mass spectrometer the data needs to be pre-processed.Open your measurement in the EpiTYPER® Analyser software and select one PCR amplicon.Manually inspect the spectra of multiple samples for irregularities by eye. For details on what to look for see Note 5. Please note that manual inspection of the spectra for measurement noise and peaks not exp […]

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INSPEcT institution(s)
Center for Genomic Science of [email protected], Istituto Italiano di Tecnologia (IIT), Milano, Italy; Department of Experimental Oncology, European Institute of Oncology (IEO), Milano, Italy
INSPEcT funding source(s)
Supported by the European Community’s Seventh Framework (FP7/2007-2013) project RADIANT (grant number 305626), and a grant from the Italian Association for Cancer Research (AIRC).

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