Difference between revisions of "List of sessions"
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* Morning - RNAseq_part1 (Ian) http://data.marcottelab.org/XenBioinfo2014/pdf/RNAseq_intro_IQ.pdf | * Morning - RNAseq_part1 (Ian) http://data.marcottelab.org/XenBioinfo2014/pdf/RNAseq_intro_IQ.pdf | ||
* Afternoon - RNAseq_part2 (Virginia) http://data.marcottelab.org/XenBioinfo2014/pdf/XenopusRNAseqLecture_VS.pdf | * Afternoon - RNAseq_part2 (Virginia) http://data.marcottelab.org/XenBioinfo2014/pdf/XenopusRNAseqLecture_VS.pdf | ||
| + | **[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2 home, tool for read aligning] | ||
| + | **[http://bio.math.berkeley.edu/eXpress/overview.html eXpress home, tool for read quantification] | ||
* Evening - DEseq (Ian) http://data.marcottelab.org/XenBioinfo2014/pdf/RNAseq_recap_IQ.pdf | * Evening - DEseq (Ian) http://data.marcottelab.org/XenBioinfo2014/pdf/RNAseq_recap_IQ.pdf | ||
| + | **[http://bioconductor.org/packages/release/bioc/html/DESeq.html DESeq package home, tool for differential expression] | ||
| + | **[http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf DESeq guide (pdf)] | ||
| + | ** [http://www.bioconductor.org/packages/release/bioc/html/edgeR.html edgeR] is another program for DE analysis. It is quite similar to DESeq. | ||
== References == | == References == | ||
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= Day 5 - 5/15/2014 = | = Day 5 - 5/15/2014 = | ||
| − | * [[ | + | * [[Machine_Learning_with_MATLAB]] (Leon) |
| − | * [ | + | ** http://www.cs.waikato.ac.nz/ml/weka/ (Weka is really good program. Also [http://www.cs.waikato.ac.nz/ml/weka/book.html accompanying book] is great introductory (and reference) book for machine learning, with very very minimal 'equations' (Taejoon). |
| − | * [[ | + | * [[ChIPseq_prep_and_map]] & Visualization by IGV(Ian) |
| + | ** http://data.marcottelab.org/XenBioinfo2014/pdf/ChIP-SEQ_protocol_JCB.pdf (ChIP-seq protocol from Julie Baker lab) | ||
| + | |||
| + | == References == | ||
| + | * [http://www.cs.umd.edu/~samir/498/10Algorithms-08.pdf Top 10 Algorithms in Data Mining (Knowl Inf Syst (2008) 14:1–37)] | ||
| + | * [http://www-users.cs.umn.edu/~kumar/dmbook/ch8.pdf Chapter 8. Clustering] in 'Introduction to Data Mining' by Tan, Steinbach and Kumar | ||
= Day 6 - 5/16/2014 = | = Day 6 - 5/16/2014 = | ||
| − | * [[ | + | * MATLAB (Leon) |
| − | * [[ | + | ** http://www.mathworks.com/matlabcentral/fileexchange/32849-htk-mfcc-matlab/content/mfcc/cell2file.m |
| − | * | + | ** http://www.mathworks.com/help/matlab/import_export/write-to-delimited-data-files.html#br2ypq2-1 |
| + | ** http://www.mathworks.com/matlabcentral/fileexchange/25387-write-cell-array-to-text-file | ||
| + | * [[SNP_analysis]] (Virginia) | ||
| + | * [[ChIPseq_motif]] (Ian) | ||
| + | * BLAST_and_sequence_analysis (Taejoon) - http://data.marcottelab.org/XenBioinfo2014/pdf/XenBioinfo2014_BLAST_TK.pdf | ||
= Day 7 - 5/17/2014 = | = Day 7 - 5/17/2014 = | ||
| − | * [[ | + | * Galaxy + GeneSet enrichment (Virginia) |
| − | * [[ | + | ** http://genetrail.bioinf.uni-sb.de/ |
| + | ** http://david.abcc.ncifcrf.gov/ | ||
| + | |||
| + | * UCSC browser, etc (Ian) - http://data.marcottelab.org/XenBioinfo2014/pdf/ucsc_primer_IQ.pdf | ||
| + | * [[Microarray]] (Taejoon) | ||
| + | * [[Functional_Network]] (Taejoon) | ||
| + | * [[HowTo_MeV]] (Taejoon) | ||
| + | * [[Orthology]] (Taejoon) | ||
* [[RNAseq_assembly]] (Taejoon) | * [[RNAseq_assembly]] (Taejoon) | ||
Latest revision as of 13:26, 17 May 2014
Servers:
- 10.120.5.246 (main Linux server)
- 10.120.6.244 (second Linux server)
- 10.120.4.248 (Mac server)
Contents
Day 2 - 5/12/2014
- Intro_to_Unix_and_Scripting (Leon) -- http://data.marcottelab.org/XenBioinfo2014/pdf/SummerDay_LP.pdf (Lecture Note)
- Intro_to_Programming_and_Python (Taejoon)
- Awk (Leon)
- Xenopus_genome (Taejoon)
Day 3 - 5/13/2014
- Morning - RNAseq_part1 (Ian) http://data.marcottelab.org/XenBioinfo2014/pdf/RNAseq_intro_IQ.pdf
- Afternoon - RNAseq_part2 (Virginia) http://data.marcottelab.org/XenBioinfo2014/pdf/XenopusRNAseqLecture_VS.pdf
- Evening - DEseq (Ian) http://data.marcottelab.org/XenBioinfo2014/pdf/RNAseq_recap_IQ.pdf
- DESeq package home, tool for differential expression
- DESeq guide (pdf)
- edgeR is another program for DE analysis. It is quite similar to DESeq.
References
- Mike Gilchrist's paper for 30-min time course RNA-seq in .X tropicalis
- Mkie Blower's paper for different prep method of X. laevis egg transcripts
- Rfx2 paper (RNA-seq + ChIP-seq)
Day 4 - 5/14/2014
- Morning 1/2 - Shotgun_Proteomics_Theory (Martin)
- Morning 2/2 - Shotgun_Proteomics_Data_Process (Taejoon)
- Afternoon I - Quantitative Proteomics (Martin)
- Afternoon II - DevTimeCourse + MATLAB (Leon)
Day 5 - 5/15/2014
- Machine_Learning_with_MATLAB (Leon)
- http://www.cs.waikato.ac.nz/ml/weka/ (Weka is really good program. Also accompanying book is great introductory (and reference) book for machine learning, with very very minimal 'equations' (Taejoon).
- ChIPseq_prep_and_map & Visualization by IGV(Ian)
- http://data.marcottelab.org/XenBioinfo2014/pdf/ChIP-SEQ_protocol_JCB.pdf (ChIP-seq protocol from Julie Baker lab)
References
- Top 10 Algorithms in Data Mining (Knowl Inf Syst (2008) 14:1–37)
- Chapter 8. Clustering in 'Introduction to Data Mining' by Tan, Steinbach and Kumar
Day 6 - 5/16/2014
- MATLAB (Leon)
- SNP_analysis (Virginia)
- ChIPseq_motif (Ian)
- BLAST_and_sequence_analysis (Taejoon) - http://data.marcottelab.org/XenBioinfo2014/pdf/XenBioinfo2014_BLAST_TK.pdf
Day 7 - 5/17/2014
- Galaxy + GeneSet enrichment (Virginia)
- UCSC browser, etc (Ian) - http://data.marcottelab.org/XenBioinfo2014/pdf/ucsc_primer_IQ.pdf
- Microarray (Taejoon)
- Functional_Network (Taejoon)
- HowTo_MeV (Taejoon)
- Orthology (Taejoon)
- RNAseq_assembly (Taejoon)
