[[Python¥Ð¥¤¥ª]]¡¡[[Python¥Ð¥¤¥ª/¥Ä¡¼¥ë]]~ &counter();¡¡¡¡¡¡&lastmod();~ *ʬÀϥġ¼¥ë [#e7c82741] -[[Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation (Nature Biotechnology volume 28, pages 511–515 (2010)):https://www.nature.com/articles/nbt.1621]] -[[Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms(PubMed):https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146043/]] -[[Third-generation sequencing fireworks at Marco Island (Nature Biotechnology volume 28, pages 426–428 (2010)):https://www.nature.com/articles/nbt0510-426]] -[[Advancing RNA-Seq analysis (Nature Biotechnology volume 28, pages 421–423 (2010)):https://www.nature.com/articles/nbt0510-421]] -[[RNA-Seq¤Î¿ôÍý¡½À¸À®¥â¥Ç¥ë¤Ë¤è¤ëȯ¸½ÎÌ¿äÄê¡§¥¢¡¼¥«¥¤¥Ö - Wolfeyes Bioinformatics beta:http://yagays.github.io/blog/2013/07/14/mathematical-models-for-transcriptome-quantification-0/]] -[[Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/pdf/nihms-366741.pdf]] -[[BaseSpace ¤Ç¹Ô¤¦ RNA-seq ÆþÌç¡¡< TopHat/CufflinksÊÔ> 2015_ilmn_webinar_basespace-rna_session12.pdf:https://jp.illumina.com/content/dam/illumina-marketing/apac/japan/documents/pdf/2015_ilmn_webinar_basespace-rna_session12.pdf]] -[[RNA-Seq¡Ã¼¡À¤Â奷¡¼¥±¥ó¥µ¡¼¡¡¤ªÇº¤ß¥«¥¦¥ó¥»¥ê¥ó¥°(2013):http://www.mss.co.jp/businessfield/bioinformatics/ngs/pop_rna-seq.html]] -[[(ERANGE) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Method 2008:https://www.ncbi.nlm.nih.gov/pubmed/18516045]] -[[(ERANGE) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Method 2008 (ResearchGate copy):https://www.researchgate.net/publication/5331349_Mapping_and_quantifying_mammalian_transcriptomes_by_RNA-Seq/download]] ------------------------ **Cuffdiff (Cufflinks) [#sb90c59c] cufflinks¤Ç¥¨¥é¡¼¤¬½Ð¤ë¡£[[HISAT2-StringTie-Cuffdiff error: BAM record error: found spliced alignment without XS attribute:https://www.biostars.org/p/222849/]]¡ÊÀµ¤·¤¯¤Ï¡©¡Ë Âкö¤Ï¡¢HISAT2¤Ç¥Ñ¥é¥á¡¼¥¿--dta-cufflinks¤ò»ØÄꤹ¤ë¤³¤È ***cufflinks/cuffdiff [#ed355856] -[[cufflinks:https://github.com/cole-trapnell-lab/cufflinks]] ^[[Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks:https://www.nature.com/articles/nprot.2012.016]] -[[binary download page:http://cole-trapnell-lab.github.io/cufflinks/install/]] cuffdiff¤ò»È¤Ã¤Æ¤ß¤ë cuffdiff¤ò»È¤Ã¤Æ¤ß¤ë 2019-06-29 ºÆÅÙ¤ä¤êľ¤¹É¬Íפ¢¤ê¤½¤¦¡£¤Þ¤ºcufflinks¤Ç½¸·×¤¬É¬Íפ«¤â¡£Í×¥Á¥§¥Ã¥¯¡£ -[[Cufflinks | RNA-seq ¤òÍøÍѤ·¤¿°äÅÁ»Òȯ¸½²òÀÏ:https://bi.biopapyrus.jp/rnaseq/expression/cufflinks.html]] ¤¢¤é¤«¤¸¤áÍѰդ·¤¿sortºÑ¤ß¤Îbam¥Õ¥¡¥¤¥ëSRR4535xx.tagged.sorted.bam ¤È¥Þ¥Ã¥×s288c_3.gff¤ËÂФ·¤Æ $cuffdiff -p 32 -o ./results1 ../s288c_e.gff -L batch,chemo \ SRR453566.tagged.sorted.bam,SRR453567.tagged.sorted.bam,SRR453568.tagged.sorted.bam \ SRR453569.tagged.sorted.bam,SRR453570.tagged.sorted.bam,SRR453571.tagged.sorted.bam ¥é¥Ù¥ëÉÕ¤±-L¤ÎÅÔ¹ç¤Ç¡¢¥é¥Ù¥ë£²¼ïÎàbatch,chemo¤ËÂФ·¤Æ¡¢ÆþÎÏ¥Õ¥¡¥¤¥ëSRR453566,67,68¤òbatch¤Ë¡¢SRR453569,70,71¤òchemo¤Ë³ä¤êÅö¤Æ¤¿¡Ê¤Ï¤º¡Ë¡£¥³¥ó¥Þ¤ÎÁ°¸å¤Ï¶õÇò¤Ê¤·¡Ê¤¢¤ë¤È¥³¥Þ¥ó¥É²ò¼á¤Ç°ú¿ô¤ÎÀÚ¤ìÌܤȻפäƤ·¤Þ¤¦¤Î¤Ç¡Ë¡¡¤³¤Î-L¤ÈÆþÎÏ¥Õ¥¡¥¤¥ë¤Î¶èÀÚ¤ê¤Ë¤è¤Ã¤Æ¡¢¸å¤Î²òÀϥѥ¿¡¼¥ó¡Ê¥½¡¼¥¹¤ÎʬÎà¡Ë¤¬·è¤Þ¤ë¤Î¤ÇÍ×Ãí°Õ¡£ Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu). [10:38:24] Loading reference annotation. [10:38:25] Inspecting maps and determining fragment length distributions. [10:40:50] Modeling fragment count overdispersion. [10:42:08] Modeling fragment count overdispersion. > Map Properties: > Normalized Map Mass: 3618635.35 > Raw Map Mass: 3746966.57 > Fragment Length Distribution: Empirical (learned) > Estimated Mean: 209.34 > Estimated Std Dev: 99.53 > Map Properties: > Normalized Map Mass: 3618635.35 > Raw Map Mass: 5136465.50 > Fragment Length Distribution: Empirical (learned) > Estimated Mean: 213.53 > Estimated Std Dev: 96.07 > Map Properties: > Normalized Map Mass: 3618635.35 > Raw Map Mass: 3780062.80 > Fragment Length Distribution: Empirical (learned) > Estimated Mean: 206.94 > Estimated Std Dev: 94.02 > Map Properties: > Normalized Map Mass: 3618635.35 > Raw Map Mass: 2502112.93 > Fragment Length Distribution: Empirical (learned) > Estimated Mean: 202.52 > Estimated Std Dev: 96.05 > Map Properties: > Normalized Map Mass: 3618635.35 > Raw Map Mass: 3127907.67 > Fragment Length Distribution: Empirical (learned) > Estimated Mean: 211.12 > Estimated Std Dev: 94.18 > Map Properties: > Normalized Map Mass: 3618635.35 > Raw Map Mass: 3898613.50 > Fragment Length Distribution: Empirical (learned) > Estimated Mean: 213.42 > Estimated Std Dev: 98.72 [10:43:25] Calculating preliminary abundance estimates [10:43:25] Testing for differential expression and regulation in locus. > Processed 6278 loci. [*************************] 100% Performed 5732 isoform-level transcription difference tests Performed 0 tss-level transcription difference tests Performed 5732 gene-level transcription difference tests Performed 0 CDS-level transcription difference tests Performed 0 splicing tests Performed 0 promoter preference tests Performing 0 relative CDS output tests Writing isoform-level FPKM tracking Writing TSS group-level FPKM tracking Writing gene-level FPKM tracking Writing CDS-level FPKM tracking Writing isoform-level count tracking Writing TSS group-level count tracking Writing gene-level count tracking Writing CDS-level count tracking Writing isoform-level read group tracking Writing TSS group-level read group tracking Writing gene-level read group tracking Writing CDS-level read group tracking Writing read group info Writing run info $ cd results1 $ ls bias_params.info cds_exp.diff genes.read_group_tracking promoters.diff tss_groups.count_tracking cds.count_tracking cuffData.db isoform_exp.diff read_groups.info tss_groups.fpkm_tracking cds.diff gene_exp.diff isoforms.count_tracking run.info tss_groups.read_group_tracking cds.fpkm_tracking genes.count_tracking isoforms.fpkm_tracking splicing.diff var_model.info cds.read_group_tracking genes.fpkm_tracking isoforms.read_group_tracking tss_group_exp.diff ¤³¤ÎÎã¤Ç¤Ï¡ÊCDS¤¬½ñ¤¤¤Æ¤¤¤Ê¤¤¤Î¤Ç¡©¡Ëgene_exp.diff¤Èisoforms_exp.diff¤¬·ë²Ì¤Ë¤Ê¤Ã¤Æ¤¤¤ë¡£ gene_exp.diff¤ò¸«¤ë¤È #ref(SRR453566-cuffdiff-gene-exp-diff.png); isoforms_exp.diff¤ò¸«¤ë¤È #ref(SRR453566-cuffdiff-isoforms-exp-diff.png); ¸µÏÀʸ~ [[Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks (Nat Protoc. ; 7(3): 562–578):https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/pdf/nihms-366741.pdf]]~ ¤Ë¤è¤ë¤È¡¢¤³¤Î·ë²Ì¤Ï[[cummeRbund:https://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html]]¤Ë¤è¤Ã¤Æ²Ä»ë²½¤Ç¤¤ë¡£~ ¼ê½ç¤Ï¤¿¤È¤¨¤Ð --[[CummeRbund¤Ç°äÅÁ»Òȯ¸½¤Î¥×¥í¥Ã¥È¤ò°äÅÁ»Ò¤´¤È¤Ëʤ٤ë - Qiita:https://qiita.com/yuifu/items/cc9730f7e3a1277f6c50]] --[[cummeRbund-example-workflow.pdf:https://www.bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-example-workflow.pdf]]¡¡¸åȾ¤¬Ì¤´°À®¤ÇÅÓÃæ¤Þ¤Ç¤·¤«¤Ê¤¤¡ª¡ª --[[cummeRbund-manual.pdf:https://www.bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf]]¡¡¥Þ¥Ë¥å¥¢¥ëÉ÷¤À¤¬¼ê½ç¤â¿¾¯°Õ¼±¤·¤Æ¤¤¤ë¡© **cummeRbund¤ò»È¤¦ [#c8ee86ea] -[[Bioconductor - cummeRbund::https://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html]] -[[CummeRbund: Visualization and Exploration of Cufflinks High-throughput Sequencing Data:https://www.bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf]]¡¡¤³¤³¤Ë½Ð¤Æ¤¤¤ë¥×¥í¥»¥¹¤Ë½¾¤Ã¤Æ°Ê²¼¼Â¸³¤¹¤ë¡£ -[[cummeRbund Example Workflow:https://www.bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-example-workflow.pdf]]¡¡¤³¤ì¤Ï½ñ¤¤«¤±¤Î¾õÂ֤Τ褦¤Ç¡¢¸åȾ¤¬¶õÇò¡£ -[[¥ê¥Õ¥¡¥ì¥ó¥¹¥Þ¥Ë¥å¥¢¥ë:https://www.bioconductor.org/packages/release/bioc/manuals/cummeRbund/man/cummeRbund.pdf]] cummeRbund¤ÎÆþÎϤÏcuffDiff¤Î·ë²Ì¤Ç¡¢cummeRband¤Ç¤Î²òÀϤΤ¿¤á¤ËcuffDiff¤Ç¥é¥Ù¥ëÉÕ¤±¤ò¤·¤Æ¤¢¤ë¤³¤È¡£¤½¤Î¥é¥Ù¥ë¤ò¸µ¤Ë¡¢Èæ³Ó¤ò¼è¤Ã¤¿¤ê¤¹¤ë¡£ ¥Ç¡¼¥¿¥ë¡¼¥È SRR453566.tagged.sorted.bam SRR453567.tagged.sorted.bam ... SRR453571.tagged.sorted.bam results1 bias_params.info cds_exp.diff genes.read_group_tracking promoters.diff tss_groups.count_tracking cds.count_tracking isoform_exp.diff read_groups.info tss_groups.fpkm_tracking cds.diff gene_exp.diff isoforms.count_tracking run.info tss_groups.read_group_tracking cds.fpkm_tracking genes.count_tracking isoforms.fpkm_tracking splicing.diff var_model.info cds.read_group_tracking genes.fpkm_tracking isoforms.read_group_tracking tss_group_exp.diff ¢¬ ¤³¤Î¥ì¥Ù¥ë¤òR¤Î¥ï¡¼¥¥ó¥°¥Ç¥£¥ì¥¯¥È¥ê¤Ë¤·¤Æ¤ª¤¯¡£ R¤òµ¯Æ°¡£ > library(cummeRbund) ¥×¥í¥°¥é¥àcummRbund¤ò¥í¡¼¥É > cuff<-readCufflinks("results1") ¥Ç¥£¥ì¥¯¥È¥ê results1 ¤«¤é¥Ç¡¼¥¿ÆÉ¹þ¤ó¤Ç¥Ç¡¼¥¿¥Ù¡¼¥¹¤Ë½ñ¤¹þ¤à (Ãí) > cuff <- readCufflinks('results1', gtfFile='../s288c_e.gff')¤Ïgenome=¤¬Ìµ¤¤¤È¥À¥á¡£genome=¤Ë½ñ¤±¤ëÃͤ¬ÉÔÌÀ A character string indicating to which genome build the .gtf annotations belong (e.g. ¡Çhg19¡Ç or ¡Çmm9¡Ç) > cuff CuffSet instance with: 2 samples 6445 genes 6445 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS > disp<-dispersionPlot(genes(cuff)) > disp > dens<-csDensity(genes(cuff)) > dens > b<-csBoxplot(genes(cuff)) > b > sm<-csScatterMatrix(genes(cuff)) > sm > s<-csScatter(genes(cuff),"chemo","batch",smooth=T) chemo¤Èbatch¤Ç¤Î»¶ÉÛ¿Þ > s > dend<-csDendro(genes(cuff)) > dend > m<-MAplot(genes(cuff),"chemo","batch") > m > v<-csVolcanoMatrix(genes(cuff)) > v > mySigGeneIds<-getSig(cuff,alpha=0.05,level='genes') > lengthh(mySigGeneIds) > sigGenes<-getGenes(cuff,sigGeneIds) sigGenes CuffGeneSet instance for 3900 genes Slots: annotation fpkm repFpkm diff count isoforms CuffFeatureSet instance of size 3900 TSS CuffFeatureSet instance of size 0 CDS CuffFeatureSet instance of size 0 promoters CuffFeatureSet instance of size 3900 splicing CuffFeatureSet instance of size 0 relCDS CuffFeatureSet instance of size 3900 > head(annotation(genes(cuff))) gene_id class_code nearest_ref_id gene_short_name 1 gene_0001 <NA> <NA> PAU8 2 gene_0002 <NA> <NA> YAL067W-A 3 gene_0003 <NA> <NA> SEO1 4 gene_0004 <NA> <NA> YAL065C 5 gene_0005 <NA> <NA> YAL064W-B 6 gene_0006 <NA> <NA> TDA8 locus length coverage feature_id isoform_id seqnames 1 NC_001133.9:1806-2169 NA NA NA <NA> <NA> 2 NC_001133.9:2479-2707 NA NA NA <NA> <NA> 3 NC_001133.9:7234-9016 NA NA NA <NA> <NA> 4 NC_001133.9:11564-11951 NA NA NA <NA> <NA> 5 NC_001133.9:12045-12426 NA NA NA <NA> <NA> 6 NC_001133.9:13362-13743 NA NA NA <NA> <NA> source type start end score strand frame 1 <NA> NA NA NA NA <NA> <NA> 2 <NA> NA NA NA NA <NA> <NA> 3 <NA> NA NA NA NA <NA> <NA> 4 <NA> NA NA NA NA <NA> <NA> 5 <NA> NA NA NA NA <NA> <NA> 6 <NA> NA NA NA NA <NA> <NA> > head(fpkm(genes(cuff))) > head(count(genes(cuff))) > head(fpkm(isoforms(cuff))) > head(diffData(genes(cuff))) > head(fpkmMatrix(genes(cuff))) ¶½Ì£¤¢¤ëgene(½¸¹ç)¤ò»ØÄꤷ¤ÆÊ¬ÀϤ¹¤ë > myGeneIds <- c("gene_0010", "gene_0010", "gene_0011", "gene_0012", "gene_0013", "gene_0014", "gene_0015", "gene_0016", "gene_0017", "gene_0018", "gene_0019") ¶½Ì£¤Î¤¢¤ëgeneid¤ò¥ê¥¹¥È¤·¤¿¤â¤Î¡£¤¢¤é¤«¤¸¤áºî¤Ã¤Æ¤¢¤ë¤È¤¹¤ë¡£¤³¤³¤Ï²¾¤ÎÎã¡£ > myGenes <- getGenes(cuff,myGeneIds) > myGenes CuffGeneSet instance for 10 genes Slots: annotation fpkm repFpkm diff count isoforms CuffFeatureSet instance of size 10 TSS CuffFeatureSet instance of size 0 CDS CuffFeatureSet instance of size 0 promoters CuffFeatureSet instance of size 10 splicing CuffFeatureSet instance of size 0 relCDS CuffFeatureSet instance of size 10 > myGeneset.pluri<-getGenes(cuff,myGeneIds,sampleIdList=c("batch")) > h<-csHeatmap(myGenes,cluster='both') > h > b<-expressionBarplot(myGenes) > b > s<-csScatter(myGenes,"chemo","batch",smooth=T) > s > v<-csVolcano(myGenes,"chemo","batch") > v > ih<-csHeatmap(isoforms(myGenes),cluster='both',labRow=F) > ih > th<-csHeatmap(TSS(myGenes),cluster='both',labRow=F) > th > den<-csDendro(myGenes) > den £±¤Ä¤À¤±¤Ë¤¹¤ë > myGeneId <- c("gene_0010") 1¤Ä¤À¤±¤Ë¤¹¤ë > myGene<-getGene(cuff,myGeneId) > head(fpkm(myGene)) Ʊ¤¸¤è¤¦¤Ë»È¤¨¤ë > gl<-expressionPlot(myGene) > gl > gl.iso.rep<-expressionPlot(isoforms(myGene),replicates=T) > gb<-expressionBarplot(myGene) > gb > igb<-expressionBarplot(isoforms(myGene),replicates=T) > gp<-csPie(myGene,level="isoforms") > gp > mySigMat<-sigMatrix(cuff,level='genes',alpha=0.05) > mySigMat > mySigGeneIds<-getSig(cuff,alpha=0.05,level='genes') > head(mySigGeneIds) > chemo_vs_batch.sigIsoformIds<-getSig(cuff,x='chemo',y='batch',alpha=0.05,level='isoforms') > myDistHeat<-csDistHeat(genes(cuff)) > myDistHeat > myRepDistHeat<-csDistHeat(genes(cuff),replicates=T) > myRepDistHeat > genes.PCA<-PCAplot(genes(cuff),"PC1","PC2") > genes.PCA > genes.MDS<-MDSplot(genes(cuff)) cmdscale(d, eig = TRUE, k = 2) ¤Ç¥¨¥é¡¼: 'k' must be in {1, 2, .. n - 1} MDS(multi-dimensional scaling)¤Ï¼¡¸µ¿ô3°Ê¾å ¥¯¥é¥¹¥¿²½ > ic<-csCluster(myGenes,k=4) > ic > ic$cluster gene_0010 gene_0011 gene_0013 gene_0014 gene_0015 gene_0016 gene_0017 1 1 2 2 3 3 4 gene_0018 gene_0019 3 3 > icp<-csClusterPlot(ic) > icp Îà»÷gene¤Î¸¡½Ð > mySimilar<-findSimilar(cuff,myGeneId,n=20) > mySimilar.expression<-expressionPlot(mySimilar,logMode=T,showErrorbars=F) > mySimilar.expression > myProfile<-c(500,0,400) > mySimilar2<-findSimilar(cuff,myProfile,n=10) > mySimilar2.expression<-expressionPlot(mySimilar2,logMode=T,showErrorbars=F) > mySimilar2.expression > head(annotation(genes(cuff))) gene_id class_code nearest_ref_id gene_short_name 1 gene_0001 <NA> <NA> PAU8 2 gene_0002 <NA> <NA> YAL067W-A 3 gene_0003 <NA> <NA> SEO1 4 gene_0004 <NA> <NA> YAL065C 5 gene_0005 <NA> <NA> YAL064W-B 6 gene_0006 <NA> <NA> TDA8 locus length coverage feature_id isoform_id seqnames 1 NC_001133.9:1806-2169 NA NA NA <NA> <NA> 2 NC_001133.9:2479-2707 NA NA NA <NA> <NA> 3 NC_001133.9:7234-9016 NA NA NA <NA> <NA> 4 NC_001133.9:11564-11951 NA NA NA <NA> <NA> 5 NC_001133.9:12045-12426 NA NA NA <NA> <NA> 6 NC_001133.9:13362-13743 NA NA NA <NA> <NA> source type start end score strand frame 1 <NA> NA NA NA NA <NA> <NA> 2 <NA> NA NA NA NA <NA> <NA> 3 <NA> NA NA NA NA <NA> <NA> 4 <NA> NA NA NA NA <NA> <NA> 5 <NA> NA NA NA NA <NA> <NA> 6 <NA> NA NA NA NA <NA> <NA> ¡Á¡Á¡Á¡Á¡Á¡Á¡Á¡Á¡Á **¤â¤¦°ìÅÙÊÙ¶¯ [#y2c99830] ¤½¤ÎÁ°¤Ë -NIG¤Î¥Ñ¥¤¥×¥é¥¤¥ó¥µ¡¼¥Ó¥¹¡¡[[NGS¥¢¥×¥ê¥±¡¼¥·¥ç¥ó Pipline-Menu-wiki:http://cell-innovation.nig.ac.jp/maser/Applications/applications_top.html]]¡¢¡¡[[Äó¶¡Á´¥Ñ¥¤¥×¥é¥¤¥ó¥ê¥¹¥È All-Pipelines:http://cell-innovation.nig.ac.jp/maser_cgi/cip-pl_list_violin_ja.cgi]]¡¢¤È¡¡[[RNA-seq¤Î¥Ñ¥¤¥×¥é¥¤¥ó:http://cell-innovation.nig.ac.jp/maser/Applications/RNA-seq.html]] »²¾È -¼ç¡¡[[Tuxedo Genome Guided Transcriptome Assembly Workshop · trinityrnaseq/RNASeq_Trinity_Tuxedo_Workshop Wiki:https://github.com/trinityrnaseq/RNASeq_Trinity_Tuxedo_Workshop/wiki/Tuxedo-Genome-Guided-Transcriptome-Assembly-Workshop]] -Äɲà --[[RNA seq ¶¤Î£² ¥Þ¥Ã¥Ô¥ó¥°¤«¤éÅý·×½èÍý¤Þ¤Ç - mac¤Ç¥¤¥ó¥Õ¥©¥Þ¥Æ¥£¥¯¥¹:http://kazumaxneo.hatenablog.com/entry/2017/03/27/141521]]~ --[[RNA seq ¶¤Î£³ ¥Ò¡¼¥È¥Þ¥Ã¥×ºîÀ® - mac¤Ç¥¤¥ó¥Õ¥©¥Þ¥Æ¥£¥¯¥¹:http://kazumaxneo.hatenablog.com/entry/2017/03/29/171543]] -Äɲá¡[[RNA-seq Analysis With R/Bioconductor - The Cat Way:http://catway.jp/lecture/tohoku-u/NGS-R-Bioconductor-2nd.html]] -¤ª¤Þ¤± --Filgen.jp¤Î¥¹¥é¥¤¥É[[NGS¥Ç¡¼¥¿²òÀÏÆþÌçWeb¥»¥ß¥Ê¡¼:https://filgen.jp/Product/BioScience21-software/CLC/NGS_Web_Seminar_slide_20181126.pdf]]¡¡¡¡¥¹¥é¥¤¥Ép17,18¤Ë²òÀϤÎÁ´ÂÎÁü¤¢¤ê --Ãæ²¬¿µ¼£ [[°äÅÁ»Òȯ¸½²òÀÏÆþÌç:http://coop-math.ism.ac.jp/files/216/%E8%B3%87%E6%96%99_nakaoka.pdf]]¡¡¥¹¥é¥¤¥É13°Ê¹ß¤¬RNA-seq ¾¯¤·¸Å¤¤¤«¡© --¥¢¥á¥ê¥¨¥Õ¡¡R N A - s e q [[20150805and28_yamaguchi.pdf https://biosciencedbc.jp/gadget/human/20150805and28_yamaguchi.pdf]]