Difference between revisions of "List of sessions"
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** 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). | ** 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) | * [[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 == | == References == | ||
Revision as of 14:31, 16 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
- Motif_analysis (Ian)
- ChIPseq_peak_calling (Ian)
- BLAST_and_sequence_analysis (Taejoon)
- SNP_and_Galaxy (Virginia)
- ChIPseq_motif (Ian)
Day 7 - 5/17/2014
- Gene_enrichment_analysis (Virginia)
- Network_analysis (Taejoon)
- RNAseq_assembly (Taejoon)
