SePIA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SePIA
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Tool usage distribution map

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Associated diseases

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Popular tool citations

chevron_left Read quality control Read alignment SNV detection Normalization Known transcript quantification Gene fusion detection Differential expression Bioinformatics workflows Adapter trimming Bioinformatics workflows Spliced read alignment Variant detection chevron_right
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SePIA specifications

Information


Unique identifier OMICS_12000
Name SePIA
Alternative name Sequence Processing Integration and Analysis
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data The mandatory input files for SePIA’s first module are tab-delimited text files containing the following information: unique, per-sample IDs and the corresponding path to unprocessed .fq/.fastq file. Two optional columns can be added to provide further identification of ‘treatment’ and ‘sample’ information, which are required for differential analysis and visualization.
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
Anduril, Docker
Source code URL http://anduril.org/sepia/download.html
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Sampsa Hautaniemi

Publication for Sequence Processing Integration and Analysis

SePIA citations

 (2)
library_books

MicroRNAs regulate key cell survival pathways and mediate chemosensitivity during progression of diffuse large B cell lymphoma

2017
PMCID: 5802506
PMID: 29242506
DOI: 10.1038/s41408-017-0033-8

[…] accession: phs000532.v2.p1), and the Lymphoma/Leukemia Molecular Profiling Project (LLMPP) (n = 233) (GEO accession: GSE10846) were used. CGCI level 1 RNA-seq data were downloaded and processed with SePIA transcriptomics analysis pipeline. A web-based cutoff finder tool (http://molpath.charite.de/cutoffanalysis) was used to determine the most prognostic cutoff level for survival outcomes. Kaplan− […]

library_books

A survey of best practices for RNA seq data analysis

2016
Genome Biol
PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] target genes. Associations might be found in databases such as mirWalk [] and miRBase [] that offer target prediction according to various algorithms. Tools such as CORNA [], MMIA [, ], MAGIA [], and SePIA [] refine predictions by testing for significant associations between genes, miRNAs, pathways and GO terms, or by testing the relatedness or anticorrelation of the expression profiles of both th […]


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SePIA institution(s)
Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
SePIA funding source(s)
Supported by the Academy of Finland (Center of Excellence in Cancer Genetics Research), the Sigrid Jusélius Foundation, Finnish Cancer Associations, and Doctoral Programme in Biomedicine.

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