High Throughput Biological Data Analysis 40795 
  CE Department- Sharif University of Technology Spring - Group 1 

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Announcments

  1394-03-09 May 30, 2015 08:45 AM  
Please install the following package:

1- bcftools

  1394-03-01 May 22, 2015 11:12 AM  
Please have the following packages:

1- Cufflinks
2- Tophat
3- Bowtie2
4- FastQC
5- FASTX
6- Velvet
7- ShortRead(R)
8- Rsamtools

  1394-02-28 May 18, 2015 05:09 AM  
Assigned Papers:

1- Farid Rashidi: Primate Segmental duplications: crubiles of evolution, diversity and disease + MAUVE
2- Amir Hossein Afshin Fard: Clustering cancer gene expression data: a comparative study
3- Mansour Hasani: The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
4- Tina Khajeh: The genome of Mesobuthus martensii reveals a unique adaptation model of arthropod
5- Younes Khanbaba : The Y-chromosome point mutation rate in human
6- Fariborz Zare Pour: Large-scale whole-genome sequencing of the Icelandic population

  1394-02-27 May 17, 2015 03:01 PM  
Please have the following package installed on your computer:

http://sourceforge.net/projects/gemsim/

  1394-02-21 May 11, 2015 03:58 AM  
Problem set II is uploaded. The due data is in two weeks.

  1394-02-13 May 03, 2015 05:10 AM  
Install the following packages:

1- limmaGUI
2- GEOquery

  1394-01-31 April 20, 2015 04:03 AM  
a new package to be installed:

1- affyQCReport

  1394-01-29 April 18, 2015 04:42 AM  
Please add the following packages:

1- affy
2- limma
3- hgu133plus2cdf
4- hgu133acdf
4- reshape2
5- mammaPrintData  <-- I have it

You also need to download cell files from the following url:
http://www.bioinfbook.org/php/?q=chapter9

I have downloaded them so you may want to bring your memory stick to get it.

  1394-01-15 April 04, 2015 03:46 AM  
1- Problem set I is uploaded.
2- You have got three weeks to solve the problems.
3- Please create the directory /projects/biological_data_analysis_2015/ps1/your_name and use setwd to make it your working directory in R.
4- You will hand in a single sweave file by the due date.

  1393-12-15 March 06, 2015 08:27 PM  
For tomorrow, we also need:

genoPlotR

Please have it installed on your R.

  1393-12-15 March 06, 2015 06:55 AM  
Please install the following packages:

1- phylip
2- Rphylip (R)
3- phyclust (R)
4- SNPlocs.Hsapiens.dbSNP.20120608 (R) --> I do have the source file
5- VariantAnnotation (R)

Make sure that you can run BLAST+, clustalw, and phylip on your system.

  1393-12-12 March 03, 2015 07:03 AM  
Slides for genomics are uploaded.
We have a class from 2 to 5 tomorrow.
Please install the following packages:

1- Mauve
2-  BSgenome.Hsapiens.UCSC.hg19  <-- I forgot to include this

  1393-12-09 February 28, 2015 07:01 AM  
Softwares to be installed:

1- IGV
2- samtools
3- GATK
4- BWA

  1393-12-02 February 21, 2015 08:33 AM  
Please install the following package:

UniProt.ws

  1393-12-02 February 21, 2015 05:49 AM  
Here is the link for the course in stanford:


http://web.stanford.edu/class/cs273a/cgi-bin/index.php

  1393-11-27 February 16, 2015 06:54 AM  
Class TIME IS 13:30. Location is 006 CE Department.

  1392-12-23 March 14, 2014 12:59 AM  
Class TIME IS 13:30. Location is not fixed yet.

  1392-12-21 March 12, 2014 08:05 PM  
Softwares to be installed:

1- BLAST+
2- MUMMER
3- BOWTIE
4- TOPHAT
5 -CLUSTALW

  1392-12-21 March 12, 2014 04:17 PM  
Packages to be installed:

BSgenome.Ecoli.NCBI.20080805
ape
muscle
TxDb.Hsapiens.UCSC.hg19.knownGene
biomaRt

  1393-11-19 February 08, 2015 04:44 AM  
Some packages to be installed:

1- BSgenomes
2- Biostrings
3- BSgenome.Celegans.UCSC.ce2
4- GenomicRanges
5- ggplot2
6- igraph
7- org.Hs.eg.db

Instructor:
Seyed Abolfazl Motahari
(smotahari@gmail.com)

3 Units
16:30-18:00
Room: CE 202
















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