Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists (Q47104977)

8 January 2018

title

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists (English)

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8 January 2018

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Xun Zhu

1

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8 January 2018

Thomas K Wolfgruber

2

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8 January 2018

Austin Tasato

3

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8 January 2018

Cédric Arisdakessian

4

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8 January 2018

David G Garmire

5

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8 January 2018

Lana X Garmire

6

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8 January 2018

publication date

5 December 2017

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8 January 2018

published in

Genome Medicine

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8 January 2018

volume

9

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8 January 2018

page(s)

108

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8 January 2018

issue

1

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8 January 2018

describes a project that uses

ggplot2

object named as

ggplot2

2 references

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=5716224

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

limma

object named as

Limma

2 references

22 June 2022

https://europepmc.org/article/PMC/5716224

inferred from PubMed Central ID database lookup

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

edgeR

object named as

edgeR

EdgeR

1 reference

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

edgeR

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exact match

https://scigraph.springernature.com/pub.10.1186/s13073-017-0492-3

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cites work

Splatter: simulation of single-cell RNA sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

ASAP: a Web-based platform for the analysis and interactive visualization of single-cell RNA-seq data

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Single-cell regulome data analysis by SCRAT.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Massively parallel digital transcriptional profiling of single cells

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

KEGG: new perspectives on genomes, pathways, diseases and drugs

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Single-Cell Transcriptomics Bioinformatics and Computational Challenges

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma.

23 May 2018

1 reference

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Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

limma powers differential expression analyses for RNA-sequencing and microarray studies

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Gene Ontology Consortium: going forward

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Bayesian approach to single-cell differential expression analysis

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Accounting for technical noise in single-cell RNA-seq experiments.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Removing technical variability in RNA-seq data using conditional quantile normalization

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

A flexible R package for nonnegative matrix factorization

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

PPAR-γ agonists and their effects on IGF-I receptor signaling: Implications for cancer

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

NVP-AUY922: a novel heat shock protein 90 inhibitor active against xenograft tumor growth, angiogenesis, and metastasis

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Capturing heterogeneity in gene expression studies by surrogate variable analysis

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Nod-like proteins in immunity, inflammation and disease

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Adjusting batch effects in microarray expression data using empirical Bayes methods

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Hedgehog signalling within airway epithelial progenitors and in small-cell lung cancer

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Gene ontology: tool for the unification of biology

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Heat shock factors and the control of the stress response

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

GeneCards: integrating information about genes, proteins and diseases.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5716224

Least squares quantization in PCM

23 May 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS13073-017-0492-3

On lines and planes of closest fit to systems of points in space

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS13073-017-0492-3

Immunotherapy of tumors with autologous tumor-derived heat shock protein preparations

21 January 2018

1 reference

12 December 2020

An accurate and robust imputation method scImpute for single-cell RNA-seq data.

1 reference

12 December 2020

Integrating single-cell transcriptomic data across different conditions, technologies, and species

1 reference

12 December 2020

SAVER: gene expression recovery for single-cell RNA sequencing.

1 reference

12 December 2020

10.1186/S13073-017-0492-3

Identifiers

DOI

1 reference

8 January 2018

Dimensions Publication ID

0 references

1 reference

8 January 2018

PubMed ID

29202807

1 reference

8 January 2018