Difference between revisions of "List of sessions"
From XenopusBioinfo
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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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* [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0077700 Mkie Blower's paper for different prep method of X. laevis egg transcripts] | * [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0077700 Mkie Blower's paper for different prep method of X. laevis egg transcripts] | ||
* [http://elifesciences.org/content/3/e01439.short Rfx2 paper (RNA-seq + ChIP-seq)] | * [http://elifesciences.org/content/3/e01439.short Rfx2 paper (RNA-seq + ChIP-seq)] | ||
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= Day 4 - 5/14/2014 = | = Day 4 - 5/14/2014 = | ||
Revision as of 10:42, 15 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_Weka (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 (Ian)
- Vis_with_IGV (Ian)
References
Day 6 - 5/16/2014
- Motif_analysis (Ian)
- ChIPseq_peak_calling (Ian)
- BLAST_and_sequence_analysis (Taejoon)
Day 7 - 5/17/2014
- Gene_enrichment_analysis (Virginia)
- Network_analysis (Taejoon)
- RNAseq_assembly (Taejoon)
