Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Types of Reports I: Hands-off Report

Types of Reports I: Hands-off Report

A hand-off report, also known as a change-of-shift report, is a crucial nursing process that ensures the smooth transition of patient care responsibilities between nursing staff.
Following are the key components and categories of hand-off reports:
Purpose and Process:

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

TridentSynth: a webtool for the retrosynthesis of molecules using chimeric type I polyketide synthases and chemoenzymatic pathways.

Nucleic acids research·2026

Same author

systemPipeR: a multipurpose workflow management system for reproducible data analysis.

NAR genomics and bioinformatics·2026

Same author

Merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis.

Nature communications·2025

Same author

<i>Pseudomonas aeruginosa</i> Activates Quorum Sensing, Antioxidant Enzymes and Type VI Secretion in Response to Oxidative Stress to Initiate Biofilm Formation and Wound Chronicity.

Antioxidants (Basel, Switzerland)·2024

Same author

spatialHeatmap: visualizing spatial bulk and single-cell assays in anatomical images.

NAR genomics and bioinformatics·2024

Same author

BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale.

PLoS computational biology·2023

Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026

Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026

Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026

Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026

Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026

Same journal

Benchmarking DNA barcode decoding strategies under high error rates.

BMC bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 14, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

systemPipeR: NGS workflow and report generation environment.

Tyler W H Backman¹, Thomas Girke²

¹Institute for Integrative Genome Biology, University of California, Riverside, 1207F Genomics Building, 3401 Watkins Drive, Riverside, 92521, CA, USA.

BMC Bioinformatics

|September 22, 2016

Summary

This summary is machine-generated.

The systemPipeR package streamlines next-generation sequencing (NGS) data analysis by automating complex workflows in R/Bioconductor. This accelerates reproducible results from various NGS applications.

Keywords:

Analysis workflow ChIP-Seq Next Generation Sequencing (NGS)RNA-Seq Ribo-Seq VAR-Seq

More Related Videos

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

Detection of Targetable Alterations in Non-small Cell Lung Cancer using Next-generation Sequencing

Detection of Targetable Alterations in Non-small Cell Lung Cancer using Next-generation Sequencing

Published on: October 10, 2025

Related Experiment Videos

Last Updated: Mar 14, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

Detection of Targetable Alterations in Non-small Cell Lung Cancer using Next-generation Sequencing

Detection of Targetable Alterations in Non-small Cell Lung Cancer using Next-generation Sequencing

Published on: October 10, 2025

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Next-generation sequencing (NGS) generates vast amounts of data, posing significant analytical challenges.
Current NGS data analysis requires specialized computational expertise and struggles with integrating diverse software tools.
A need exists for automated, reproducible, and efficient end-to-end analysis workflows within the R/Bioconductor environment.

Purpose of the Study:

To develop an integrated R/Bioconductor package for automating next-generation sequencing (NGS) data analysis.
To provide a flexible and extensible environment for building and executing comprehensive NGS workflows.
To facilitate automated report generation and simplify the analysis of common NGS applications.

Main Methods:

Developed systemPipeR, an R/Bioconductor package offering a unified interface for NGS workflow construction.
Implemented automated report generation capabilities for analysis results.
Supported integration of R and command-line tools for local and cluster computing.
Included a flexible sample annotation system for complex experimental designs.
Provided pre-configured workflows for RNA-Seq, ChIP-Seq, VAR-Seq, and Ribo-Seq.

Main Results:

systemPipeR enables the creation and execution of end-to-end NGS analysis workflows.
The package offers automated report generation and supports diverse computational environments.
It simplifies complex sample set management through its annotation infrastructure.
Pre-configured templates accelerate the analysis of key NGS applications like RNA-Seq and ChIP-Seq.

Conclusions:

systemPipeR significantly accelerates the generation of reproducible analysis results from NGS experiments.
It efficiently leverages existing R/Bioconductor and command-line tools without restricting user choices.
The package enhances the accessibility and efficiency of NGS data analysis for researchers.
systemPipeR is freely available from Bioconductor for all major operating systems.