Tag: Workflow

CellVGAE – Unsupervised scRNA-seq analysis Workflow with Graph Attention Networks

CellVGAE

:: DESCRIPTION

CellVGAE uses the connectivity between cells (such as k-nearest neighbour graphs or KNN) with gene expression values as node features to learn high-quality cell representations in a lower-dimensional space, with applications in downstream analyses like (density-based) clustering, visualisation, gene set enrichment analysis and others.

::DEVELOPER

CellVGAE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

CellVGAE

:: MORE INFORMATION

Citation:

Buterez D, Bica I, Tariq I, Andrés-Terré H, Liò P.
CellVGAE: an unsupervised scRNA-seq analysis workflow with graph attention networks.
Bioinformatics. 2021 Dec 2:btab804. doi: 10.1093/bioinformatics/btab804. Epub ahead of print. PMID: 34864884.

MuWU v1.1.1 – Mu-seq Workflow Utility

MuWU v1.1.1

:: DESCRIPTION

MuWU is an automated Mutant-seq workflow utility initially created for the identification of Mutator insertion sites of the BonnMu resource, representing a reverse genetics mutant collection for functional genetics in maize (Zea mays).

::DEVELOPER

Tyll Stöcker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Python
:: DOWNLOAD

MuWU

:: MORE INFORMATION

Citation

Stöcker T, Altrogge L, Marcon C, Win YN, Hochholdinger F, Schoof H.
MuWU: Mutant-seq library analysis and annotation.
Bioinformatics. 2021 Sep 29:btab679. doi: 10.1093/bioinformatics/btab679. Epub ahead of print. PMID: 34586393.

MitoScape v1.0 – Machine-learning workflow for Aligning mtDNA from NGS data

MitoScape v1.0

:: DESCRIPTION

MitoScape is a novel, big-data, software for extracting mitochondrial DNA sequences from NGS.

::DEVELOPER

Larry N. Singh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MitoScape

:: MORE INFORMATION

Citation

Singh LN, Ennis B, Loneragan B, Tsao NL, Lopez Sanchez MIG, Li J, Acheampong P, Tran O, Trounce IA, Zhu Y, Potluri P; Regeneron Genetics Center, Emanuel BS, Rader DJ, Arany Z, Damrauer SM, Resnick AC, Anderson SA, Wallace DC.
MitoScape: A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data.
PLoS Comput Biol. 2021 Nov 11;17(11):e1009594. doi: 10.1371/journal.pcbi.1009594. Epub ahead of print. PMID: 34762648.

systemPipeR 1.27.27 – NGS Workflow and report Generation Environment

systemPipeR 1.27.27

:: DESCRIPTION

systemPipeR is an R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

systemPipeR

:: MORE INFORMATION

Citation

H Backman TW, Girke T.
systemPipeR: NGS workflow and report generation environment.
BMC Bioinformatics. 2016 Sep 20;17:388. doi: 10.1186/s12859-016-1241-0. PMID: 27650223; PMCID: PMC5029110.

Wildfire/GEL 2.0 – Build Workflows

Wildfire/GEL 2.0

:: DESCRIPTION

Wildfire is a graphical tool for building workflows. It comes preconfigured to use EMBOSS programs as components for Bioinformatics workflows, and is extensible to support other components.

GEL (Grid Execution Language) is a general-purpose parallel scripting language for describing workflows. It features explicit parallel constructs which allow for efficient parallel execution on clusters, Grids and SMP machines. There is GEL support for Condor Grids, and SGE, PBS and LSF-based clusters.

Wildfire/GEL provides an integrated solution for building and executing workflows. Wildfire runs as an application on desktop and laptop platforms, and the GEL workflows can either run on the same machine or remotely on the Grid or on a cluster

::DEVELOPER

Bioinformatics Institute of Singapore.

:: SCREENSHOTS

 

:: REQUIREMENTS

  • Windows / Linux
  • Java

:: DOWNLOAD

 Wildfire/GEL

:: MORE INFORMATION

Citation:

Francis Tang , Ching Lian Chua , Liang-Yoong Ho , Yun Ping Lim , Praveen Issac and Arun Krishnan
Wildfire: distributed, Grid-enabled workflow construction and execution,
BMC Bioinformatics 2005, 6:69.

Chua Ching Lian , Francis Tang , Praveen Issac , Arun Krishnan
GEL: Grid Execution Language,
J. Parallel and Distributed Computing 2005, 65(7):857-869.

Taverna 2.5 – Workflow Management System

Taverna 2.5

:: DESCRIPTION

Taverna project aims to provide a language and software tools to facilitate easy use of workflow and distributed compute technology within the eScience community.

::DEVELOPER

Taverna Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Taverna

:: MORE INFORMATION

Citation:

D. Hull, K. Wolstencroft, R. Stevens, C. Goble, M. Pocock, P. Li, and T. Oinn,
“Taverna: a tool for building and running workflows of services.,”
Nucleic Acids Research, vol. 34, iss. Web Server issue, pp. 729-732, 2006.

T. Oinn, M. Greenwood, M. Addis, N. Alpdemir, J. Ferris, K. Glover, C. Goble, A. Goderis, D. Hull, D. Marvin, P. Li, P. Lord, M. Pocock, M. Senger, R. Stevens, A. Wipat, and C. Wroe,
“Taverna: lessons in creating a workflow environment for the life sciences,”
Concurrency and Computation: Practice and Experience, vol. 18, iss. 10, pp. 1067-1100, 2006.

ballaxy – Galaxy-based workflow toolkit for Structural Bioinformatics

ballaxy

:: DESCRIPTION

ballaxy is a workflow framework for structure based computational biology based on the Galaxy workflow engine.

::DEVELOPER

BALL Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Windows
  • Web Server
  • C++ Comipiler

:: DOWNLOAD

 ballaxy

:: MORE INFORMATION

Citation:

ballaxy: web services for structural bioinformatics.
Hildebrandt AK, Stöckel D, Fischer NM, de la Garza L, Krüger J, Nickels S, Röttig M, Schärfe C, Schumann M, Thiel P, Lenhof HP, Kohlbacher O, Hildebrandt A.
Bioinformatics. 2014 Sep 2. pii: btu574.

LONI Pipeline 7.0.3 – Free Workflow Application

LONI Pipeline 7.0.3

:: DESCRIPTION

The LONI Pipeline is a free workflow application primarily aimed at computational scientists. With the LONI Pipeline, users can quickly create workflows that take advantage of all the greatest tools available in neuroimaging, genomics, bioinformatics, etc.

::DEVELOPER

Laboratory of Neuro Imaging

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • JRE

:: DOWNLOAD

 LONI Pipeline

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jul 26;12:304. doi: 10.1186/1471-2105-12-304.
Applications of the pipeline environment for visual informatics and genomics computations.
Dinov ID1, Torri F, Macciardi F, Petrosyan P, Liu Z, Zamanyan A, Eggert P, Pierce J, Genco A, Knowles JA, Clark AP, Van Horn JD, Ames J, Kesselman C, Toga AW.

AffyPipe – Pipeline for Affymetrix Axiom Genotyping Workflow

AffyPipe

:: DESCRIPTION

AffyPipe allows you to edit SNP probe classes directly while exporting genotypes in PLINK format

::DEVELOPER

AffyPipe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux
  • Python

:: DOWNLOAD

 AffyPipe

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Nov 1;30(21):3118-9. doi: 10.1093/bioinformatics/btu486.
AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow.
Nicolazzi EL, Iamartino D, Williams JL

kronos 2.3.0 – Workflow Assembler for Cancer Genome Analytics and Informatics

kronos 2.3.0

:: DESCRIPTION

Kronos is a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

kronos

:: MORE INFORMATION

Citation

Gigascience. 2017 Jul 1;6(7):1-10. doi: 10.1093/gigascience/gix042.
Kronos: a workflow assembler for genome analytics and informatics.
Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP

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