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Stem Cell Transcriptional Networks

Overview of attention for book
Cover of 'Stem Cell Transcriptional Networks'

Table of Contents

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    Book Overview
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    Chapter 1 Efficient library preparation for next-generation sequencing analysis of genome-wide epigenetic and transcriptional landscapes in embryonic stem cells.
  3. Altmetric Badge
    Chapter 2 Analysis of next-generation sequencing data using galaxy.
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    Chapter 3 edgeR for Differential RNA-seq and ChIP-seq Analysis: An Application to Stem Cell Biology.
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    Chapter 4 Use Model-Based Analysis of ChIP-Seq (MACS) to Analyze Short Reads Generated by Sequencing Protein-DNA Interactions in Embryonic Stem Cells.
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    Chapter 5 Spatial Clustering for Identification of ChIP-Enriched Regions (SICER) to Map Regions of Histone Methylation Patterns in Embryonic Stem Cells
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    Chapter 6 Identifying Stem Cell Gene Expression Patterns and Phenotypic Networks with AutoSOME
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    Chapter 7 Visualization and Clustering of High-Dimensional Transcriptome Data Using GATE
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    Chapter 8 Interpreting and Visualizing ChIP-seq Data with the seqMINER Software.
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    Chapter 9 A Description of the Molecular Signatures Database (MSigDB) Web Site
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    Chapter 10 Use of Genome-Wide RNAi Screens to Identify Regulators of Embryonic Stem Cell Pluripotency and Self-Renewal
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    Chapter 11 Correlating Histone Modification Patterns with Gene Expression Data During Hematopoiesis
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    Chapter 12 In Vitro Maturation and In Vitro Fertilization of Mouse Oocytes and Preimplantation Embryo Culture
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    Chapter 13 Derivation and manipulation of trophoblast stem cells from mouse blastocysts.
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    Chapter 14 Conversion of epiblast stem cells to embryonic stem cells using growth factors and small molecule inhibitors.
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    Chapter 15 Generation of Induced Pluripotent Stem Cells Using Chemical Inhibition and Three Transcription Factors
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    Chapter 16 Transdifferentiation of Mouse Fibroblasts and Hepatocytes to Functional Neurons
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    Chapter 17 Direct Lineage Conversion of Pancreatic Exocrine to Endocrine Beta Cells In Vivo with Defined Factors
  19. Altmetric Badge
    Chapter 18 Direct Reprogramming of Cardiac Fibroblasts to Cardiomyocytes Using MicroRNAs.
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    Chapter 19 Reprogramming Somatic Cells into Pluripotent Stem Cells Using miRNAs.
Attention for Chapter 2: Analysis of next-generation sequencing data using galaxy.
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  • Above-average Attention Score compared to outputs of the same age and source (56th percentile)

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Chapter title
Analysis of next-generation sequencing data using galaxy.
Chapter number 2
Book title
Stem Cell Transcriptional Networks
Published in
Methods in molecular biology, January 2014
DOI 10.1007/978-1-4939-0512-6_2
Pubmed ID
Book ISBNs
978-1-4939-0511-9, 978-1-4939-0512-6
Authors

Daniel Blankenberg, Jennifer Hillman-Jackson, Blankenberg, Daniel, Hillman-Jackson, Jennifer

Abstract

The extraordinary throughput of next-generation sequencing (NGS) technology is outpacing our ability to analyze and interpret the data. This chapter will focus on practical informatics methods, strategies, and software tools for transforming NGS data into usable information through the use of a web-based platform, Galaxy. The Galaxy interface is explored through several different types of example analyses. Instructions for running one's own Galaxy server on local hardware or on cloud computing resources are provided. Installing new tools into a personal Galaxy instance is also demonstrated.

X Demographics

X Demographics

The data shown below were collected from the profiles of 3 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 80 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 1%
United States 1 1%
Brazil 1 1%
Unknown 77 96%

Demographic breakdown

Readers by professional status Count As %
Researcher 25 31%
Student > Ph. D. Student 12 15%
Student > Master 11 14%
Student > Bachelor 8 10%
Professor > Associate Professor 4 5%
Other 7 9%
Unknown 13 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 22 28%
Biochemistry, Genetics and Molecular Biology 17 21%
Computer Science 7 9%
Medicine and Dentistry 5 6%
Immunology and Microbiology 4 5%
Other 9 11%
Unknown 16 20%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 13 October 2020.
All research outputs
#15,299,919
of 22,754,104 outputs
Outputs from Methods in molecular biology
#5,313
of 13,089 outputs
Outputs of similar age
#190,001
of 305,238 outputs
Outputs of similar age from Methods in molecular biology
#200
of 597 outputs
Altmetric has tracked 22,754,104 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 13,089 research outputs from this source. They receive a mean Attention Score of 3.3. This one is in the 45th percentile – i.e., 45% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 305,238 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 27th percentile – i.e., 27% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 597 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 56% of its contemporaries.