scholarly journals LAVA: a streamlined visualization tool for longitudinal analysis of viral alleles

2019 ◽  
Author(s):  
Michelle J. Lin ◽  
Ryan C. Shean ◽  
Negar Makhsous ◽  
Alexander L. Greninger
Keyword(s):  
Genome Evolution ◽  
Longitudinal Analysis ◽  
Viral Evolution ◽  
Read Depth ◽  
Visualization Tool ◽  
Command Line ◽  
Interactive Analysis ◽  
Command Line Tool ◽  
User Friendly ◽  
Over Time

AbstractWith their small genomes, fast evolutionary rates, and clinical significance, viruses have long been fodder for studies of whole genome evolution. One common need in these studies is the analysis of viral evolution over time through longitudinal sampling. However, there exists no simple tool to automate such analyses. We created a simple command-line visualization tool called LAVA (Longitudinal Analysis of Viral Alleles). LAVA allows dynamic and interactive visualization of viral evolution across the genome and over time. Results are easily shared via a single HTML file that also allows interactive analysis based on read depth and allele frequency. LAVA requires minimal input and runs in minutes for most use cases. LAVA is programmed mainly in Python 3 and is compatible with Mac and Linux machines. LAVA is a user-friendly command-line tool for generating, visualizing, and sharing the results of longitudinal viral genome evolution analysis. Instructions for downloading, installing, and using LAVA can be found at https://github.com/michellejlin/lava.

scholarly journals Visualization of circular RNAs and their internal splicing events from transcriptomic data

2020 ◽  
Vol 36 (9) ◽  
pp. 2934-2935 ◽  
Author(s):  
Yi Zheng ◽  
Fangqing Zhao
Keyword(s):  
Supplementary Information ◽  
Circular Rnas ◽  
Visualization Tool ◽  
Command Line ◽  
Supplementary Data ◽  
Transcriptomic Data ◽  
Command Line Tool ◽  
Transcriptome Comparison ◽  
Multiple Samples ◽  
Splicing Patterns

Abstract Summary Circular RNAs (circRNAs) are proved to have unique compositions and splicing events distinct from canonical mRNAs. However, there is no visualization tool designed for the exploration of complex splicing patterns in circRNA transcriptomes. Here, we present CIRI-vis, a Java command-line tool for quantifying and visualizing circRNAs by integrating the alignments and junctions of circular transcripts. CIRI-vis can be applied to visualize the internal structure and isoform abundance of circRNAs and perform circRNA transcriptome comparison across multiple samples. Availability and implementation https://sourceforge.net/projects/ciri/files/CIRI-vis. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MakeHub: Fully automated generation of UCSC Genome Browser Assembly Hubs

2019 ◽  
Author(s):  
Katharina J. Hoff
Keyword(s):  
Genome Annotation ◽  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Visualization Tool ◽  
Command Line ◽  
The Novel ◽  
Automated Generation ◽  
Genome Visualization ◽  
Command Line Tool ◽  
Tool Assembly

AbstractNovel genomes are today often annotated by small consortia or individuals whose background is not from bioinformatics. This audience requires tools that are easy to use. This need had been addressed by several genome annotation tools and pipelines. Visualizing resulting annotation is a crucial step of quality control. The UCSC Genome Browser is a powerful and popular genome visualization tool. Assembly Hubs allow browsing genomes that are hosted locally via already available UCSC Genome Browser servers. The steps for creating custom Assembly Hubs are well documented and the required tools are publicly available. However, the number of steps for creating a novel Assembly Hub is large. In some cases the format of input files needs to be adapted which is a difficult task for scientists without programming background. Here, we describe the novel command line tool MakeHub that generates Assembly Hubs for the UCSC Genome Browser in a fully automated fashion. The pipeline also allows extending previously created Hubs by additional tracks.MakeHub is freely available for download from https://github.com/Gaius-Augustus/[email protected]

scholarly journals PrimeDesign software for rapid and simplified design of prime editing guide RNAs

2020 ◽  
Author(s):  
Jonathan Y. Hsu ◽  
Andrew V. Anzalone ◽  
Julian Grünewald ◽  
Kin Chung Lam ◽  
Max W. Shen ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Web Application ◽  
Saturation Mutagenesis ◽  
Command Line ◽  
Searchable Database ◽  
Guide Rna ◽  
Guide Rnas ◽  
Genome Wide ◽  
Command Line Tool ◽  
User Friendly

AbstractPrime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we also constructed PrimeVar, the first comprehensive and searchable database for prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations to install or correct >68,500 pathogenic human genetic variants from the ClinVar database.

scholarly journals PrimeDesign software for rapid and simplified design of prime editing guide RNAs

2020 ◽  
Author(s):  
Jonathan Hsu ◽  
Julian Grünewald ◽  
Regan Szalay ◽  
Justine Shih ◽  
Andrew Anzalone ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Web Application ◽  
Saturation Mutagenesis ◽  
Command Line ◽  
Guide Rna ◽  
Guide Rnas ◽  
Pathogenic Variants ◽  
Genome Wide ◽  
Command Line Tool ◽  
User Friendly

Abstract Prime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we constructed PrimeVar, a comprehensive and searchable database that includes candidate prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations for installing or correcting >68,500 pathogenic human genetic variants from the ClinVar database. Finally, we used PrimeDesign to design pegRNAs/ngRNAs to install a variety of human pathogenic variants in human cells.

scholarly journals CIAlign - A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments

2020 ◽  
Author(s):  
Charlotte Tumescheit ◽  
Andrew E. Firth ◽  
Katherine Brown
Keyword(s):  
Command Line ◽  
Sequence Alignments ◽  
Bioinformatics Analyses ◽  
Multiple Sequence ◽  
Biologically Relevant ◽  
Multiple Sequence Alignments ◽  
Before And After ◽  
Command Line Tool ◽  
User Friendly ◽  
Low Coverage

AbstractBackgroundThroughout biology, multiple sequence alignments (MSAs) form the basis of much investigation into biological features and relationships. These alignments are at the heart of many bioinformatics analyses. However, sequences in MSAs are often incomplete or very divergent, which leads to poorly aligned regions or large gaps in alignments. This slows down computation and can impact conclusions without being biologically relevant. Therefore, cleaning the alignment by removing these regions can substantially improve analyses.ResultsWe present a comprehensive, user-friendly MSA trimming tool with multiple visualisation options. Our highly customisable command line tool aims to give intervention power to the user by offering various options, and outputs graphical representations of the alignment before and after processing to give the user a clear overview of what has been removed.The main functionalities of the tool include removing regions of low coverage due to insertions, removing gaps, cropping poorly aligned sequence ends and removing sequences that are too divergent or too short. The thresholds for each function can be specified by the user and parameters can be adjusted to each individual MSA. CIAlign is complementary to existing alignment trimming tools, with an emphasis on solving specific and common alignment problems and on providing transparency to the user.ConclusionCIAlign effectively removes poorly aligned regions and sequences from MSAs and provides novel visualisation options. This tool can be used to improve the alignment quality for further analysis and processing. The tool is aimed at anyone who wishes to automatically clean up parts of an MSA and those requiring a new, accessible way for visualising large MSAs.

scholarly journals User-friendly, scalable tools and workflows for single-cell analysis

2020 ◽  
Author(s):  
P. Moreno ◽  
N. Huang ◽  
J.R. Manning ◽  
S. Mohammed ◽  
A. Solovyev ◽  
...  
Keyword(s):  
Data Analysis ◽  
Single Cell ◽  
Programming Languages ◽  
Single Cell Analysis ◽  
Command Line ◽  
Cell Analysis ◽  
Rna Seq ◽  
Interactive Analysis ◽  
User Friendly ◽  
Analysis Environment

AbstractSingle-cell RNA-Seq (scRNA-Seq) data analysis requires expertise in command-line tools, programming languages and scaling on compute infrastructure. As scRNA-Seq becomes widespread, computational pipelines need to be more accessible, simpler and scalable. We introduce an interactive analysis environment for scRNA-Seq, based on Galaxy, with ~70 functions from major single-cell analysis tools, which can be run on compute clusters, cloud providers or single machines, to bring compute to the data in scRNA-Seq.

scholarly journals PrimeDesign software for rapid and simplified design of prime editing guide RNAs

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonathan Y. Hsu ◽  
Julian Grünewald ◽  
Regan Szalay ◽  
Justine Shih ◽  
Andrew V. Anzalone ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Web Application ◽  
Saturation Mutagenesis ◽  
Command Line ◽  
Guide Rna ◽  
Guide Rnas ◽  
Pathogenic Variants ◽  
Genome Wide ◽  
Command Line Tool ◽  
User Friendly

AbstractPrime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we construct PrimeVar, a comprehensive and searchable database that includes candidate prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations for installing or correcting >68,500 pathogenic human genetic variants from the ClinVar database. Finally, we use PrimeDesign to design pegRNAs/ngRNAs to install a variety of human pathogenic variants in human cells.

scholarly journals Visual4DTracker: a tool to interact with 3D + t image stacks

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ermanno Cordelli ◽  
Paolo Soda ◽  
Giulio Iannello
Keyword(s):  
Synthetic Data ◽  
Time Lapse ◽  
Temporal Data ◽  
Image Stack ◽  
Biological Phenomena ◽  
Insulin Granules ◽  
Matlab Package ◽  
User Friendly ◽  
Drosophila Cells ◽  
Over Time

Abstract Background Biological phenomena usually evolves over time and recent advances in high-throughput microscopy have made possible to collect multiple 3D images over time, generating $$3D+t$$ 3 D + t (or 4D) datasets. To extract useful information there is the need to extract spatial and temporal data on the particles that are in the images, but particle tracking and feature extraction need some kind of assistance. Results This manuscript introduces our new freely downloadable toolbox, the Visual4DTracker. It is a MATLAB package implementing several useful functionalities to navigate, analyse and proof-read the track of each particle detected in any $$3D+t$$ 3 D + t stack. Furthermore, it allows users to proof-read and to evaluate the traces with respect to a given gold standard. The Visual4DTracker toolbox permits the users to visualize and save all the generated results through a user-friendly graphical user interface. This tool has been successfully used in three applicative examples. The first processes synthetic data to show all the software functionalities. The second shows how to process a 4D image stack showing the time-lapse growth of Drosophila cells in an embryo. The third example presents the quantitative analysis of insulin granules in living beta-cells, showing that such particles have two main dynamics that coexist inside the cells. Conclusions Visual4DTracker is a software package for MATLAB to visualize, handle and manually track $$3D+t$$ 3 D + t stacks of microscopy images containing objects such cells, granules, etc.. With its unique set of functions, it remarkably permits the user to analyze and proof-read 4D data in a friendly 3D fashion. The tool is freely available at https://drive.google.com/drive/folders/19AEn0TqP-2B8Z10kOavEAopTUxsKUV73?usp=sharing

Long-Run Effects in Dynamic Systems: New Tools for Cross-Lagged Panel Models

2021 ◽  
pp. 109442812199322
Author(s):  
Ali Shamsollahi ◽  
Michael J. Zyphur ◽  
Ozlem Ozkok
Keyword(s):  
Recent Work ◽  
Dynamic Systems ◽  
Quantitative Methods ◽  
Simulated Dataset ◽  
Impulse Responses ◽  
Panel Models ◽  
Long Run ◽  
Short Run ◽  
User Friendly ◽  
Over Time

Cross-lagged panel models (CLPMs) are common, but their applications often focus on “short-run” effects among temporally proximal observations. This addresses questions about how dynamic systems may immediately respond to interventions, but fails to show how systems evolve over longer timeframes. We explore three types of “long-run” effects in dynamic systems that extend recent work on “impulse responses,” which reflect potential long-run effects of one-time interventions. Going beyond these, we first treat evaluations of system (in)stability by testing for “permanent effects,” which are important because in unstable systems even a one-time intervention may have enduring effects. Second, we explore classic econometric long-run effects that show how dynamic systems may respond to interventions that are sustained over time. Third, we treat “accumulated responses” to model how systems may respond to repeated interventions over time. We illustrate tests of each long-run effect in a simulated dataset and we provide all materials online including user-friendly R code that automates estimating, testing, reporting, and plotting all effects (see https://doi.org/10.26188/13506861 ). We conclude by emphasizing the value of aligning specific longitudinal hypotheses with quantitative methods.

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