Bioinformatics Software: Sequence Analysis
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Bioinformatics Software: Sequence Analysis
Research and postings on the latest in bioinformatic analysis software that's out there/published and open source. Let's not re-invent the wheel. Disclaimer: I do not promote one software over the next, you'll have to evaluate software on your own.
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StatQuest: PCA clearly explained | RNA-Seq Blog

StatQuest: PCA clearly explained | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
RNA-seq results often contain a PCA or MDS plot. This StatQuest explains how these graphs are generated, how to interpret them, and how to determine if the plot
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Mark Pitman's curator insight, December 3, 2016 9:41 AM

PCA is an important tool in data analysis and has broad application in different bioinformatics workflows. Learn more about it in this overview. 

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DEIVA – a web application for interactive visual analysis of differential gene expression profiles | RNA-Seq Blog

Differential gene expression (DGE) analysis is a technique to identify statistically significant differences in RNA abundance for genes or arbitrary features
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CATchUP – A web database for spatiotemporally regulated genes | RNA-Seq Blog

CATchUP – A web database for spatiotemporally regulated genes | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
For proper control of biological activity, some key genes are highly expressed in a particular spatiotemporal domain. Mining of such spatiotemporally expressed
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RNA-Seq analysis is easy as 1-2-3 | RNA-Seq Blog

The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with counts summarised at the gene
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SCnorm – A quantile-regression based approach for robust normalization of single-cell RNA-seq data | RNA-Seq Blog

SCnorm – A quantile-regression based approach for robust normalization of single-cell RNA-seq data | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
Normalization of RNA-sequencing data is essential for accurate downstream inference, but the assumptions upon which most methods are based do not hold in the
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Perturb-seq – Enables Large-Scale Analysis of Complex Genetic Interactions Using CRISPR-Based Gene Perturbation and Single-Cell RNA Sequencing | RNA-Seq Blog

Perturb-seq – Enables Large-Scale Analysis of Complex Genetic Interactions Using CRISPR-Based Gene Perturbation and Single-Cell RNA Sequencing | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
Researchers from UC San Francisco and the Broad Institute of MIT and Harvard have developed a new method for performing high-throughput functional screening of
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MAV-seq – Management, Analysis and Visualization of Sequence Data | RNA-Seq Blog

MAV-seq – Management, Analysis and Visualization of Sequence Data | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
The increasing amount of heterogeneous Next Generation Sequencing (NGS) data generated today necessitates a robust platform for the efficient data storage,
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Acfs: accurate circRNA identification and quantification from RNA-Seq data

Acfs: accurate circRNA identification and quantification from RNA-Seq data | Bioinformatics Software: Sequence Analysis | Scoop.it
Circular RNAs (circRNAs) are a group of single-stranded RNAs in closed circular form.
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CountClust – Visualizing the Structure of RNA-seq Expression Data using Grade of Membership Models | RNA-Seq Blog

CountClust – Visualizing the Structure of RNA-seq Expression Data using Grade of Membership Models | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
Grade of membership models, also known as "admixture models", "topic models" or "Latent Dirichlet Allocation", are a generalization of cluster models that allow
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How well do RNA-Seq differential gene expression tools perform in higher eukaryotes? | RNA-Seq Blog

How well do RNA-Seq differential gene expression tools perform in higher eukaryotes? | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
RNA-seq experiments are usually carried out in three or fewer replicates. In order to work well with so few samples, Differential Gene Expression (DGE) tools
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InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data

Analysis of fusion transcripts has become increasingly important due to their link with cancer development. Since high-throughput sequencing approaches survey fusion events exhaustively, several computational methods for the detection of gene fusions from RNA-seq data have been developed. This kind of analysis, however, is complicated by native trans-splicing events, the splicing-induced complexity of the transcriptome and biases and artefacts introduced in experiments and data analysis. There are a number of tools available for the detection of fusions from RNA-seq data; however, certain differences in specificity and sensitivity between commonly used approaches have been found. The ability to detect gene fusions of different types, including isoform fusions and fusions involving non-coding regions, has not been thoroughly studied yet. Here, we propose a novel computational toolkit called InFusion for fusion gene detection from RNA-seq data. InFusion introduces several unique features, such as discovery of fusions involving intergenic regions, and detection of anti-sense transcription in chimeric RNAs based on strand-specificity. Our approach demonstrates superior detection accuracy on simulated data and several public RNA-seq datasets. This improved performance was also evident when evaluating data from RNA deep-sequencing of two well-established prostate cancer cell lines. InFusion identified 26 novel fusion events that were validated in vitro, including alternatively spliced gene fusion isoforms and chimeric transcripts that include intergenic regions. The toolkit is freely available to download from http:/bitbucket.org/kokonech/infusion.
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SCODE – An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation | RNA-Seq Blog

SCODE – An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
The analysis of RNA-Seq data from individual differentiating cells enables us to reconstruct the differentiation process and the degree of differentiation (in
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Analysis of EBV Transcription Using High-Throughput RNA Sequencing | RNA-Seq Blog

Analysis of EBV Transcription Using High-Throughput RNA Sequencing | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
High-throughput sequencing of RNA is used to analyze the transcriptomes of viruses and cells, providing information about transcript structure and abundance. A
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TBro – visualization and management of de novo transcriptomes | RNA-Seq Blog

TBro – visualization and management of de novo transcriptomes | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost
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iSmaRT – a toolkit for a comprehensive analysis of small RNA-Seq data | RNA-Seq Blog

The interest in investigating the biological roles of small non-coding RNAs (sncRNAs) is increasing, due to the pleiotropic effects of these molecules exert in
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Using Single Nucleotide Variations in Single-Cell RNA-Seq to Identify Tumor Subpopulations and Genotype-phenotype Linkage

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases | RNA-Seq Blog

The species-specific plant Pathway Genome Databases (PGDBs) based on the BioCyc platform provide a conceptual model of the cellular metabolic network of an
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Comprehensive benchmarking of RNA-Seq aligners | RNA-Seq Blog

Comprehensive benchmarking of RNA-Seq aligners | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline
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Analysis of Annotation and Differential Expression Methods used in RNA-Seq Studies | RNA-Seq Blog

Analysis of Annotation and Differential Expression Methods used in RNA-Seq Studies | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
Major advances in sequencing technology have contributed to the ability to examine complex patterns of genome activity in a wide range of organisms that are
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lncScore: alignment-free identification of long noncoding RNA from assembled novel transcripts

lncScore: alignment-free identification of long noncoding RNA from assembled novel transcripts | Bioinformatics Software: Sequence Analysis | Scoop.it
RNA-Seq based transcriptome assembly has been widely used to identify novel lncRNAs.
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TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

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SeqPlots – Interactive software for exploratory data analyses, pattern discovery and visualization in genomics | RNA-Seq Blog

Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of
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A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor | RNA-Seq Blog

Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be
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Docker Pipelines for RNA-Seq Alignment and Analyses | RNA-Seq Blog

Background: Docker (https://www.docker.com) is an application that packages binary executables and scripts into modules (containers) with their software
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VirusDetect – a new pipeline for virus identification | RNA-Seq Blog

VirusDetect – a new pipeline for virus identification | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
Researchers studying the viruses that affect agricultural production or human health now have a new tool for investigating where viruses have spread, on a local
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TACO – a computational method to reconstruct a consensus transcriptome from multiple RNA-seq data sets | RNA-Seq Blog

TACO – a computational method to reconstruct a consensus transcriptome from multiple RNA-seq data sets | RNA-Seq Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
Accurate transcript structure and abundance inference from RNA sequencing (RNA-seq) data is foundational for molecular discovery. Here researchers from the
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