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

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Announcments

  1395-05-12 August 02, 2016 05:24 PM  
Please be at Professor Motahari's office according to the following schedule in order to present your project and report.

On Wednesday - 95/05/13

Group 1: 10:00-10:15
Group 3: 10:15-10:30
Group 4: 10:30-10:45
Group 5: 10:45-11:00
Group 6: 11:00-11:15
Group 7: 11:15-11:30

  1395-05-11 August 01, 2016 07:21 PM  
The Grades of assignment 3 are ready. You can find them in Grades Section.

  1395-05-10 July 31, 2016 10:36 AM  
The Grades of assignment 4 are ready. You can find them in Grades Section.

  1395-05-08 July 29, 2016 11:33 PM  
The grades of assignment 2 are ready. You can find them in Grades Section.

  1395-05-11 August 01, 2016 07:24 PM  
The grades of assignment 5 are ready. You can find them in Grades Section.

  1395-02-18 May 07, 2016 04:51 PM  
Make sure to have "sangerseqR" package in R. you may need the following package to be able to install "sangerseqR" package:
htmltools
httpuv
jsonlite
mime
R6
shiny
I will upload the compiled version of all this dependencies for Rstudio v3.2 in Ubuntu so you can copy them in R/../3.2/ or install them directly from bioconductor.
You can find a tutorial for this package in Resources.
A Homework will be uploaded for this package soon.
- Afshinfard

  1394-12-21 March 11, 2016 08:45 PM  
These are the packages you have to install on your shell (Terminal)

MUMmer (http://mummer.sourceforge.net)
Bowtie1 (http://bowtie-bio.sourceforge.net/index.shtml)
Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
TopHat (https://ccb.jhu.edu/software/tophat/index.shtml)
Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/)
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
FASTX (http://hannonlab.cshl.edu/fastx_toolkit/download.html)
ClustalW (http://www.clustal.org/clustal2/)
IGV (http://en.bio-soft.net/format/igv.html)
Samtools (https://sourceforge.net/projects/samtools/?source=navbar)
GATK (https://www.broadinstitute.org/gatk/download/)
BWA (http://bio-bwa.sourceforge.net)
Mauve (http://en.bio-soft.net/format/Mauve.html)
Velvet (https://www.ebi.ac.uk/~zerbino/velvet/)
BCFtools (http://www.htslib.org/download/)
BLAST+ (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/)

  1394-12-01 February 20, 2016 04:26 PM  
Make sure you have the following packages in RStudio:
(I can give you them at Lab 802 and you can copy them to your computer)

BSgenomes
Biostrings
GenomicRanges
muscle
biomaRt
BSgenome.Celegans.UCSC.ce2
BSgenome.Ecoli.NCBI.20080805
org.Hs.eg.db
TxDb.Hsapiens.UCSC.hg19.knownGene
BSgenome.Hsapiens.UCSC.hg19
SNPlocs.Hsapiens.dbSNP.20120608
UniProt.ws
VariantAnnotation
affyQCReport
affy
limma
hgu133plus2cdf
hgu133acdf
mammaPrintData
GEOquery
ShortRead
Rsamtools
————————————
ggplot2
igraph
ape
Rphylip
phyclust
genoPlotR
reshape2

Instructor:
Seyed Abolfazl Motahari
(motahari@sharif.edu)

3 Units
Sat. Mon. 4:30-5:45
















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