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Rolando Garcia-Milian's blog

(2 X 2) 2 High-throughput Data Analysis Workshops X 2 on NCBI Public Databases.

19 September 2016 - 10:09am by Rolando Garcia-Milian

Cushing/Whitney Medical Library has organized these four workshops, two of them on high-throughput data analysis tools and two on NCBI public databases. Although these are free and open to any Yale affiliate, registration is required due to limited seating.  

Title:      NGS Data Analysis in Partek® Software: Onsite Workshop

Registration: http://schedule.yale.edu/event/2819565


Morning Session (Overview, Hands On: Analysis on RNA-Seq Data): 9:00AM – 12:00PM

Fall Training Sessions on Bioinformatics at the Medical Library

6 September 2016 - 10:40pm by Rolando Garcia-Milian

The Yale Medical Library is offering a number of bioinformatics training session this Fall. These sessions are free and open to any Yale affiliate but registration is required due to limited seating.

Please contact Rolando.milian@yale.edu  for questions or comments.


Title: The VERY Basics of the Unix Command Line

Access to Partek Flow for the analysis of NGS data available to Yale biomedical researchers

8 July 2016 - 2:11pm by Rolando Garcia-Milian

The Yale Medical Library is providing access to Partek Flow, a Graphical User Interface and user-friendly software for the analysis of RNA, SmallRNA, and DNA sequencing experiments. A webinar showing how to use this software will take place in SHM C-103 on August 4, 2016 (see details below).

Webinar: NGS Data Analysis in Partek Software

Registration here

Day of Data 2016 Spring Discussion Series: Outcome Defined Organization of Patient Profiles

25 April 2016 - 11:48am by Rolando Garcia-Milian

The Day of Data 2016 Spring Discussion Series will feature Dr. Alexander Cloninger. Dr. Cloninger has active applied collaborations with medical researchers at the Center for Outcomes Research and Evaluation at Yale and the National Institutes of Health. His current research deals with defining and analyzing patient similarity for the purposes of clustering and outcome prediction.

Four On-site Workshops on Next-Generation Sequencing Data Analysis Tools

20 April 2016 - 10:10am by Rolando Garcia-Milian

The End-user Bioinformatics Program at the Yale Cushing/Medical Library is hosting these four workshops on tools for the analysis of NGS data. Besides the two trainings on tools for functional analysis of NGS data already supported by the Medical Library (Ingenuity Pathway Analysis and MetaCore), we will have a presentation on Partek Flow, and another one on CLC Bio (QIAGEN). The medical library will ask for feedback on these tools for future support and licensing. If you are interested in attending any of these presentations, please register to reserve your seat.

The Yale Medical Library is Providing Access to the Human Gene Mutation Database (HGMD®)

17 April 2016 - 9:45pm by Rolando Garcia-Milian

As part of its End-user Bioinformatics Program, the Cushing Whitney Medical Library is providing access to the the Human Gene Mutation Database (HGMD®) to all Yale affiliates. This database organizes all known genotypes responsible for causing human inherited disease along with disease-associated polymorphisms published in the peer-reviewed literature— HGMD mutation data are manually curated from the scientific literature.

On-site NCBI Bioinformatics Workshop at Yale School of Medicine

24 February 2016 - 2:00pm by Rolando Garcia-Milian

On April 5 and 6, Dr. Peter Cooper*** will provide training in the form of four workshops (see below) on the some of the most valuable National Center for Biotechnology Information bioinformatics resources and tools at Yale School of Medicine. This training is hosted by the Yale Cushing/Whitney Medical Library. Although free and open to any Yale affiliate, it is recommended to register since seating is limited.  

DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources (DECIPHER)

6 January 2016 - 1:41pm by Rolando Garcia-Milian

Many genetic variants are novel or rare which makes difficult their clinical interpretation. The DECIPHER Consortium was initiated in 2004 as a community of academic centers of Clinical Genetics who submit consented, anonymized  genotype  and  phenotype  data  from  patients  with  rare  genomic  disorders for sharing with other clinicians and researchers.

Do not let Excel to deplete your gene list

24 November 2015 - 3:25pm by Rolando Garcia-Milian

Last night, while preparing an RNAseq dataset for functional analysis. I found this problem again. When opening high-throughput data results into Excel be aware that this software will convert (by default) some gene symbols into a date format- see examples in the table below. These conversions are not reversible so the original name cannot be recovered. Zeeberg et al. reported this problem back in 2004.

Get your omics functional analysis done: upcoming trainings on Ingenuity Pathway Analysis and MetaCore

15 October 2015 - 4:45pm by Rolando Garcia-Milian

The Yale Medical Library is providing to all Yale affiliates free access to two of the most powerful commercial bioinformatics tools for the analysis of omics data: MetaCore and Ingenuity Pathway Analysis. This is part of a pilot project conducted by the medical library in order to find sustainable and long term access to these tools. Please register for these upcoming trainings if you are interested in learning how to use these tools or if you need a refresher.

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