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UTAP: User-friendly Transcriptome Analysis Pipeline

Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran, Dena Leshkowitz
2019 BMC Bioinformatics  
Conclusion: Our User-friendly Transcriptome Analysis Pipeline (UTAP) is an open source, web-based intuitive platform available to the biomedical research community, enabling researchers to efficiently  ...  Results: In order to enable fast and user-friendly data analysis, we developed an intuitive and scalable transcriptome pipeline that executes the full process, starting from cDNA sequences derived by RNA-Seq  ...  Availability of data and materials Information about where to download the UTAP Docker application can be found at https://utap.readthedocs.io.  ... 
doi:10.1186/s12859-019-2728-2 fatcat:6ytquwm2nbgmzntbiknqaluaei

RASflow: an RNA-Seq analysis workflow with Snakemake

Xiaokang Zhang, Inge Jonassen
2020 BMC Bioinformatics  
Utilizing the workflow management system Snakemake and the package management system Conda, we have developed a modular, flexible and user-friendly RNA-Seq analysis workflow: RNA-Seq Analysis Snakemake  ...  To be applicable for a wide variety of applications, RASflow supports the mapping of reads to both genomic and transcriptomic assemblies.  ...  We would also like to thank the research school NORBIS where XZ took the training on analysis of next generation sequencing.  ... 
doi:10.1186/s12859-020-3433-x pmid:32183729 fatcat:er5sv5jf6vhz5jlmupgy4chzf4

LSTrAP-Cloud: A User-Friendly Cloud Computing Pipeline to Infer Coexpression Networks

Qiao Wen Tan, William Goh, Marek Mutwil
2020 Genes  
In order to facilitate gene function prediction, we show how our user-friendly pipeline, the Large-Scale Transcriptomic Analysis Pipeline in Cloud (LSTrAP-Cloud), can be useful in helping biologists make  ...  The LSTrAP-Cloud is based on Google Colaboratory, and provides user-friendly tools that process quality-control RNA sequencing data streamed from the European Nucleotide Archive.  ...  Furthermore, multiple user-friendly pipelines are an invaluable resource both for experts and nonbioinformaticians, to which pipelines such as UTAP [25] , LSTrAP-Lite [24] , and LSTrAP [26] are made  ... 
doi:10.3390/genes11040428 pmid:32316247 pmcid:PMC7230309 fatcat:7s7nnr2swnfq3ndnpbinegbn24

LSTrAP-Cloud: A User-friendly Cloud Computing Pipeline to Infer Co-functional and Regulatory Networks [article]

Qiao Wen Tan, William Goh, Marek Mutwil
2020 bioRxiv   pre-print
In order to facilitate gene function prediction, we show how our user-friendly pipeline, Large-Scale Transcriptomic Analysis Pipeline in Cloud (LSTrAP-Cloud), can be useful in helping biologists make a  ...  LSTrAP-Cloud is based on Google Colaboratory and provides user-friendly tools that process and quality-control RNA sequencing data streamed from the European Sequencing Archive.  ...  UTAP: User-friendly Transcriptome Analysis Pipeline. BMC Bioinformatics 2019, 20, 154. Vaneechoutte, D.; Vandepoele, K.  ... 
doi:10.1101/2020.03.11.986794 fatcat:ae6qgp65hnf6hloixlr2ze3thq

RASflow: An RNA-Seq Analysis Workflow with Snakemake [article]

Xiaokang Zhang, Inge Jonassen
2019 bioRxiv   pre-print
Results: Utilizing the workflow management system Snakemake and the package management system Conda, we have developed a modular, flexible and user-friendly RNA-Seq analysis pipeline: RNA-Seq Analysis  ...  To be applicable for a wide variety of applications, RASflow supports mapping of reads to both genomic and transcriptomic assemblies.  ...  We would also like to thank the research school NORBIS where XZ took the training on analysis of next generation sequencing.  ... 
doi:10.1101/839191 fatcat:a4kli36hsbc7jpks2iqffi2hou

Transcriptome profiling research in urothelial cell carcinoma [article]

Umar Ahmad, Buhari Ibrahim, Mustapha Mohammed, Ahmed Faris Aldoghachi, Mahmood Usman, Abdulbasit Haliru Yakubu, Abubakar Sadiq Tanko, Khadijat Abubakar Bobbo, Usman Adamu Garkuwa, Abdullahi Adamu Faggo, Sagir Mustapha, Mahmoud Al-Masaeed (+3 others)
2021 arXiv   pre-print
We list the commonly used computational platforms and software that are publicly available for RNA-Seq analysis.  ...  Keywords: Transcriptome profiling, RNA-sequencing, genomics, bioinformatics, bladder cancer  ...  User-friendly Transcriptome Analysis Pipeline) is an open source, web-based intuitive and scalable transcriptome pipeline that executes the full process, starting from sequences (RNA-Seq and bulk MARS-Seq  ... 
arXiv:2011.10372v4 fatcat:mavw6o43wbcl3jfdmqrpuzg57y

Ultradian rhythms of AKT phosphorylation and gene expression emerge in the absence of the circadian clock components Per1 and Per2

Rona Aviram, Vaishnavi Dandavate, Gal Manella, Marina Golik, Gad Asher, Samer Hattar
2021 PLoS Biology  
Importantly, the liver transcriptome of Per1,2−/− mice also showed ultradian rhythms, corresponding to pAKT rhythmicity and consisting of AKT-related genes and regulators.  ...  Processing of raw sequencing data into read counts was performed via the User-friendly Transcriptome Analysis Pipeline (UTAP) [56] .  ...  The pipeline quantifies genes annotated in RefSeq (that have expanded with 1,000 bases toward 5 0 edge and 100 bases toward 3 0 bases).  ... 
doi:10.1371/journal.pbio.3001492 pmid:34968386 pmcid:PMC8718012 fatcat:k4mvrw5tavd7vk2x5vhv2huw3y

BiSEK: a platform for a reliable differential expression analysis [article]

Roni Haas, Dean Light, Yahav Festinger, Neta Friedman, Ayelet T. Lamm
2021 bioRxiv   pre-print
Here we present Biological Sequence Expression Kit (BiSEK), a graphical user interface-based platform for DEA, dedicated to a reliable inquiry.  ...  ABSTRACTDifferential Expression Analysis (DEA) of RNA-sequencing data is frequently performed for detecting key genes, affected across different conditions.  ...  For DEA based on RNA-seq, a typical pre-processing pipeline includes: 1. Mapping of RNA-seq reads to the genome or the transcriptome 2.  ... 
doi:10.1101/2021.02.22.432271 fatcat:cyiv7mmtlnbgfllh5lbvvliyja

Circulating miR-181 is a prognostic biomarker for amyotrophic lateral sclerosis [article]

Iddo Magen, Anna Maria Laura Coenen-Stass, Nancy S Yacovzada, Julian Grosskreutz, Ching-Hua Lu, Linda Greensmith, Andrea Malaspina, Pietro Fratta, Eran Hornstein
2019 bioRxiv   pre-print
Crucially, we conduct our analysis also on longitudinal samples reflecting disease progression, and are able to integrate detailed clinical phenotyping in our analysis.  ...  Fastq files were demultiplexed using the User-friendly Transcriptome Analysis All rights reserved. No reuse allowed without permission.  ...  Pipeline (UTAP) developed at the Weizmann Institute(27). Human exact mature miRNA . https://doi.org/10.1101/833079 doi: bioRxiv preprint 1 6 4 C. W. Law, Y. Chen, W. Shi, G. K.  ... 
doi:10.1101/833079 fatcat:tggw24atvrgqpkooyxcko2wtla

Classification and prediction of frontotemporal dementia based on plasma microRNAs [article]

Iddo Magen, Nancy Yacovzada, Jason D Warren, Carolin Heller, Imogen Swift, Yoana Bobeva, Andrea Malaspina, Jonathan D Rohrer, Pietro Fratta, Eran Hornstein
2020 medRxiv   pre-print
The analysis revealed the diagnostic importance of 20 circulating endogenous miRNAs in distinguishing FTD cases from controls.  ...  Fastq files were demultiplexed using the User-friendly Transcriptome Analysis 283 Pipeline (UTAP) developed at the Weizmann Institute (34).  ...  Sequences were mapped to the 284 human genome using Qiagen GeneGlobe analysis web tool. an Alzheimer's Society grant (AS-PG-16-007).  ... 
doi:10.1101/2020.01.22.20018408 fatcat:ojlaey4jhjaprnyhswztb2wsli