scholarly journals ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in

2019 ◽  
Author(s):  
Hongjian Jin ◽  
Lawryn H Kasper ◽  
Jon D Larson ◽  
Gang Wu ◽  
Suzanne J Baker ◽  
...  
Keyword(s):  
Histone Modification ◽  
Histone Modifications ◽  
In Silico ◽  
Peak Detection ◽  
Normalization Method ◽  
Supplementary Information ◽  
Global Changes ◽  
Supplementary Data ◽  
Similar Magnitude ◽  
Scaling Factors

Abstract Motivation The traditional reads per million normalization method is inappropriate for the evaluation of ChIP-seq data when treatments or mutations have global effects. Changes in global levels of histone modifications can be detected with exogenous reference spike-in controls. However, most ChIP-seq studies overlook the normalization that must be corrected with spike-in. A method that retrospectively renormalizes datasets without spike-in is lacking. Results ChIPseqSpikeInFree is a novel ChIP-seq normalization method to effectively determine scaling factors for samples across various conditions and treatments, which does not rely on exogenous spike-in chromatin or peak detection to reveal global changes in histone modification occupancy. Application of ChIPseqSpikeInFree on five datasets demonstrates that this in silico approach reveals a similar magnitude of global changes as the spike-in method does. Availability and implementation St. Jude Cloud (https://pecan.stjude.cloud/permalink/spikefree) and St. Jude Github ( https://github.com/stjude/ChIPseqSpikeInFree). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals NACHO: an R package for quality control of NanoString nCounter data

2019 ◽  
Author(s):  
Mickaël Canouil ◽  
Gerard A Bouland ◽  
Amélie Bonnefond ◽  
Philippe Froguel ◽  
Leen M ’t Hart ◽  
...  
Keyword(s):  
Quality Control ◽  
R Package ◽  
Third Parties ◽  
Supplementary Information ◽  
Expression Data ◽  
Supplementary Data ◽  
Scaling Factors ◽  
Comprehensive Method ◽  
Normalization Methods

Abstract Summary The NanoStringTM nCounter® is a platform for the targeted quantification of expression data in biofluids and tissues. While software by the manufacturer is available in addition to third parties packages, they do not provide a complete quality control (QC) pipeline. Here, we present NACHO (‘NAnostring quality Control dasHbOard’), a comprehensive QC R-package. The package consists of three subsequent steps: summarize, visualize and normalize. The summarize function collects all the relevant data and stores it in a tidy format, the visualize function initiates a dashboard with plots of the relevant QC outcomes. It contains QC metrics that are measured by default by the manufacturer, but also calculates other insightful measures, including the scaling factors that are needed in the normalization step. In this normalization step, different normalization methods can be chosen to optimally preprocess data. Together, NACHO is a comprehensive method that optimizes insight and preprocessing of nCounter® data. Availability and implementation NACHO is available as an R-package on CRAN and the development version on GitHub https://github.com/mcanouil/NACHO. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Differentially conserved amino acid positions may reflect differences in SARS-CoV-2 and SARS-CoV behaviour

2021 ◽  
Author(s):  
Denisa Bojkova ◽  
Jake E McGreig ◽  
Katie-May McLaughlin ◽  
Stuart G Masterson ◽  
Magdalena Antczak ◽  
...  
Keyword(s):  
Cell Culture ◽  
Amino Acid ◽  
In Silico ◽  
Virus Entry ◽  
Genomic Variation ◽  
Supplementary Information ◽  
Cell Tropism ◽  
Supplementary Data ◽  
Biological Behaviour ◽  
Novel Coronavirus

Abstract Motivation SARS-CoV-2 is a novel coronavirus currently causing a pandemic. Here, we performed a combined in-silico and cell culture comparison of SARS-CoV-2 and the closely related SARS-CoV. Results Many amino acid positions are differentially conserved between SARS-CoV-2 and SARS-CoV, which reflects the discrepancies in virus behaviour, i.e. more effective human-to-human transmission of SARS-CoV-2 and higher mortality associated with SARS-CoV. Variations in the S protein (mediates virus entry) were associated with differences in its interaction with ACE2 (cellular S receptor) and sensitivity to TMPRSS2 (enables virus entry via S cleavage) inhibition. Anti-ACE2 antibodies more strongly inhibited SARS-CoV than SARS-CoV-2 infection, probably due to a stronger SARS-CoV-2 S-ACE2 affinity relative to SARS-CoV S. Moreover, SARS-CoV-2 and SARS-CoV displayed differences in cell tropism. Cellular ACE2 and TMPRSS2 levels did not indicate susceptibility to SARS-CoV-2. In conclusion, we identified genomic variation between SARS-CoV-2 and SARS-CoV that may reflect the differences in their clinical and biological behaviour. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Epidemiological modeling in StochSS Live!

2021 ◽  
Author(s):  
Richard Jiang ◽  
Bruno Jacob ◽  
Matthew Geiger ◽  
Sean Matthew ◽  
Bryan Rumsey ◽  
...  
Keyword(s):  
Stochastic Model ◽  
Epidemiological Model ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Web Based ◽  
Epidemiological Modeling ◽  
Modeling Simulation ◽  
Wide Range ◽  
Biochemical Systems

Abstract Summary We present StochSS Live!, a web-based service for modeling, simulation and analysis of a wide range of mathematical, biological and biochemical systems. Using an epidemiological model of COVID-19, we demonstrate the power of StochSS Live! to enable researchers to quickly develop a deterministic or a discrete stochastic model, infer its parameters and analyze the results. Availability and implementation StochSS Live! is freely available at https://live.stochss.org/ Supplementary information Supplementary data are available at Bioinformatics online.

KEC: unique sequence search by K-mer exclusion

2021 ◽  
Author(s):  
Pavel Beran ◽  
Dagmar Stehlíková ◽  
Stephen P Cohen ◽  
Vladislav Čurn
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Source Code ◽  
Unique Sequence ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Laptop Computers ◽  
Sequence Search ◽  
Target Sequences ◽  
Cross Reference

Abstract Summary Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences. Due to its speed, it can be used for datasets of genomic size and can be run on desktop or laptop computers with modest specifications. Availability and implementation KEC is freely available for non-commercial purposes. Source code and executable binary files compiled for Linux, Mac and Windows can be downloaded from https://github.com/berybox/KEC. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

2020 ◽  
Author(s):  
Matteo Chiara ◽  
Federico Zambelli ◽  
Marco Antonio Tangaro ◽  
Pietro Mandreoli ◽  
David S Horner ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Ad Hoc ◽  
State Of The Art ◽  
Supplementary Information ◽  
Genomic Sequences ◽  
Supplementary Data ◽  
Evolutionary Patterns ◽  
Genomic Variants ◽  
Art Methods ◽  
Available Resources

Abstract Summary While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2. Availabilityand implementation Galaxy   http://corgat.cloud.ba.infn.it/galaxy; software: https://github.com/matteo14c/CorGAT/tree/Revision_V1; docker: https://hub.docker.com/r/laniakeacloud/galaxy_corgat. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals UniBioDicts: Unified access to Biological Dictionaries

2020 ◽  
Author(s):  
John Zobolas ◽  
Vasundra Touré ◽  
Martin Kuiper ◽  
Steven Vercruysse
Keyword(s):  
User Interface ◽  
Life Science ◽  
Biological Data ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Query Interface ◽  
Controlled Vocabularies ◽  
Search String ◽  
Software Packages ◽  
The Right

Abstract Summary We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts or UBDs) provide a single query-interface for accessing the online API services of leading biological data providers. Given a search string, UBDs return a list of matching term, identifier and metadata units from databases (e.g. UniProt), controlled vocabularies (e.g. PSI-MI) and ontologies (e.g. GO, via BioPortal). This functionality can be connected to input fields (user-interface components) that offer autocomplete lookup for these dictionaries. UBDs create a unified gateway for accessing life science concepts, helping curators find annotation terms across resources (based on descriptive metadata and unambiguous identifiers), and helping data users search and retrieve the right query terms. Availability and implementation The UBDs are available through npm and the code is available in the GitHub organisation UniBioDicts (https://github.com/UniBioDicts) under the Affero GPL license. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CONCUR: quick and robust calculation of codon usage from ribosome profiling data

2020 ◽  
Author(s):  
Michaela Frye ◽  
Susanne Bornelöv
Keyword(s):  
Codon Usage ◽  
Ribosome Profiling ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Usage Analysis

Abstract Summary CONCUR is a standalone tool for codon usage analysis in ribosome profiling experiments. CONCUR uses the aligned reads in BAM format to estimate codon counts at the ribosome E-, P- and A-sites and at flanking positions. Availability and implementation CONCUR is written in Perl and is freely available at https://github.com/susbo/concur. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MorphOT: transport-based interpolation between EM maps with UCSF ChimeraX

2020 ◽  
Author(s):  
Arthur Ecoffet ◽  
Frédéric Poitevin ◽  
Khanh Dao Duc
Keyword(s):  
Optimal Transport ◽  
Three Dimensional ◽  
Linear Interpolation ◽  
The Other ◽  
Supplementary Information ◽  
Conformational Heterogeneity ◽  
Supplementary Data ◽  
Image Dataset ◽  
Standard Linear ◽  
Unique Potential

Abstract Motivation Cryogenic electron microscopy (cryo-EM) offers the unique potential to capture conformational heterogeneity, by solving multiple three-dimensional classes that co-exist within a single cryo-EM image dataset. To investigate the extent and implications of such heterogeneity, we propose to use an optimal-transport-based metric to interpolate barycenters between EM maps and produce morphing trajectories. Results While standard linear interpolation mostly fails to produce realistic transitions, our method yields continuous trajectories that displace densities to morph one map into the other, instead of blending them. Availability and implementation Our method is implemented as a plug-in for ChimeraX called MorphOT, which allows the use of both CPU or GPU resources. The code is publicly available on GitHub (https://github.com/kdd-ubc/MorphOT.git), with documentation containing tutorial and datasets. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals BioCommons: a robust java library for RNA structural bioinformatics

2021 ◽  
Author(s):  
Tomasz Zok
Keyword(s):  
Source Code ◽  
Structural Bioinformatics ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Bioinformatic Tools ◽  
Data Formats ◽  
Central Repository ◽  
Diverse Data ◽  
2D And 3D ◽  
Java Library

Abstract Motivation Biomolecular structures come in multiple representations and diverse data formats. Their incompatibility with the requirements of data analysis programs significantly hinders the analytics and the creation of new structure-oriented bioinformatic tools. Therefore, the need for robust libraries of data processing functions is still growing. Results BioCommons is an open-source, Java library for structural bioinformatics. It contains many functions working with the 2D and 3D structures of biomolecules, with a particular emphasis on RNA. Availability and implementation The library is available in Maven Central Repository and its source code is hosted on GitHub: https://github.com/tzok/BioCommons Supplementary information Supplementary data are available at Bioinformatics online.

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