About

Bioinformatics & Biostatistics

Description

The Bioinformatics & Biostatistics Shared Resource (BSR) provides essential services and technical support for all aspects of bioinformatics & biostatistics for CSHL Cancer Center members. From providing advice at the planning stages of data-intensive experiments to developing customized software tools for analyzing data, the BSR works closely with Cancer Center members to support CSHL research projects. We also encourage Cancer Center members to learn the basic techniques of bioinformatic & biostatistic analysis. The BSR is happy to guide Cancer Center members in the use of web-based interfaces to sophisticated computational tools, enabling CSHL researchers to do much of the analysis on their own.

 

Services

Custom Software Development


The Bioinformatics & Biostatistics Shared Resource provides custom software consulting and data mining services for a variety of specialized scientific applications. Whether your experiment is still in the planning stages or data generation has been completed, our staff can provide advice, assistance and analysis.

 

Shared BioComputing Software


The BSR maintains a selected list of web resources (CSHL internal link) for common bioinformatics & biostatistics tasks. For more computationally intensive procedures, the BSR maintains a private Galaxy server (CSHL internal link) that gives Cancer Center researchers a user-friendly interface to sophisticated data analysis tools running on the High Performance Computing Cluster.

 
Training


The BSR runs periodic campus-wide training courses in basic bioinformatics & biostatistics techniques and resources both within and outside the CSHL campus. Contact the BSR for assistance with local software installations or for individual training sessions.

 

Standard Analysis:
1. Bulk
  • RNA-Seq
  • Quality control, Alignment, Quantification, Regression, Differential analysis, Pathway Analysis, and Visualization
  • ATAC-Seq
  • ChIP-Seq
  • DNA-Seq
  • Quality control, Alignment, Variant calling 
2. Single-cell
  • RNA-seq
  • Quality control, Alignment, Quantification, Regression, Dimensionality reduction, Clustering, Marker Identification, Pathway Analysis, and Visualization
  • ATAC-Seq
  • Multimodal/Multiomics
  • DNA-seq
  • Quality control, Alignment, Variant calling
 
Non-Standard Analysis:
Standard analysis without alignment, Pseudoalignment, Public database (ex. TCGA), New tools implementation, Gene regulatory, etc.
  
Custom Script Writing:
By request, we can create customized scripts for specific and user-friendly implementation (R and Python)
 
Consulting:
We provide consulting sessions to help researchers in designing experiments, data extraction, quality control, analysis strategy, visualization, and project ideas. The first session is free and then charged for follow-up sessions (see rates)
 
Self-service:
Users can do limited analysis independently by using Galaxy online. Website: http://galaxy.seqomics.cshl.edu 
Differential analysis and complimentary visualization/plots. Website: https://debrowser.umassmed.edu

Leadership

W. Richard McCombie, Ph.D.

 

Location and hours of operation

Hours Location Appointment
Mon.-Fri. 9am - 5pm Koch & Woodbury Genome Center, Room 191 NA
Bioinformatics Office Hours, Tuesday 2pm - 4pm Woodbury Genome Center, Room 191 https://calendly.com/utama/bioinformatics-office-hours
Biostatistics Office Hours, Thursday 2pm - 4pm Koch https://calendly.com/cshlbiostat

 

Links and Resources

  1. Web resources: http://intranet.cshl.edu/research/shared-resources/bioinformatics-shared-resource
  2. Private Galaxy server: http://galaxy.seqomics.cshl.edu
     

Contacts

Name Role Phone Email Location
Raditya Utama
Bioinformatician
 
850-524-3763
 
Utama@cshl.edu
 
Woodbury Genome Center, Room 191
 
Alex Dobin
Head
 

 
dobin@cshl.edu
 
Woodbury Genome Center
 
Taehoon Ha
Biostatistician
 

 
ha@cshl.edu
 
Koch
 

Services


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