eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing. (Q30769819)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

review article

1 reference

title

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

0 references

1 reference

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

Rachel L Dittmar

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

author name string

Tiezheng Yuan

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

Meijun Du

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

Manish Kohli

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

Lisa Boardman

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

Stephen N Thibodeau

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

Liang Wang

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

language of work or name

English

0 references

publication date

5 March 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

volume

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

page(s)

176

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

9 March 2020

DESeq2

object named as

R package DESeq

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Assessment of transcript reconstruction methods for RNA-seq

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

Systematic evaluation of spliced alignment programs for RNA-seq data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

TCW: transcriptome computational workbench

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

miRspring: a compact standalone research tool for analyzing miRNA-seq data.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

Characterization of human plasma-derived exosomal RNAs by deep sequencing.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

Differential analysis of gene regulation at transcript resolution with RNA-seq

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

Fast gapped-read alignment with Bowtie 2

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

Ten years of pathway analysis: current approaches and outstanding challenges

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

Chipster: user-friendly analysis software for microarray and other high-throughput data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

A pipeline for RNA-seq data processing and quality assessment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

New methods for next generation sequencing based microRNA expression profiling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

miRBase: integrating microRNA annotation and deep-sequencing data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

Differential expression analysis for sequence count data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

mirTools: microRNA profiling and discovery based on high-throughput sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

DSAP: deep-sequencing small RNA analysis pipeline

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

An introduction to recursive partitioning: rationale, application, and characteristics of classification and regression trees, bagging, and random forests

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

The Sequence Alignment/Map format and SAMtools

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4029068

miRNAkey: a software for microRNA deep sequencing analysis

20 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-15-176

Computational analysis of RNA-seq

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-15-176

GeneProf: analysis of high-throughput sequencing experiments

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24593312

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-15-176

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

9 March 2020

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1471-2164-15-176

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

PubMed publication ID

24593312

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24593312%20AND%20SRC:MED&resulttype=core&format=json