Mini-Tutorals - Revision history

Wikiuser: /* ospC amplicon identification */

2025-11-16T04:13:57Z

ospC amplicon identification

@@ Line 915: / Line 915: @@
 </syntaxhighlight>
-=ospC amplicon identification=
+=Amplicon NGS sequencing=
 <syntaxhighlight lang="bash">
 #Index nucleotide file:

2025-08-07T11:07:29Z

Exploratory sequence analysis in R (seqinr package)

← Older revision		Revision as of 11:07, 7 August 2025
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	* Gene family databases: https://doua.prabi.fr/main/index		* Gene family databases: https://doua.prabi.fr/main/index
	* Tutorial:		* Tutorial:
			* Hogenom: bacterial (13 phylum) homolog databases: http://hogenom.univ-lyon1.fr/

	=Genome viewer=		=Genome viewer=
	# geneviewer is an R package https://wiki.genometracker.org/index.php?title=Mini-Tutorals&action=edit&section=1for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, perform...		# geneviewer is an R package https://wiki.genometracker.org/index.php?title=Mini-Tutorals&action=edit&section=1for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, perform...

2025-08-07T10:51:39Z

Genome viewer

← Older revision		Revision as of 10:51, 7 August 2025
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			=Exploratory sequence analysis in R (seqinr package)=
			* Help page: https://cran.r-project.org/web/packages/seqinr/refman/seqinr.html
			* Gene family databases: https://doua.prabi.fr/main/index
			* Tutorial:
	=Genome viewer=		=Genome viewer=
	# geneviewer is an R package ~~for~~ plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, perform...		# geneviewer is an R package https://wiki.genometracker.org/index.php?title=Mini-Tutorals&action=edit&section=1for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, perform...
	# Ref: https://nvelden.github.io/geneviewer/articles/geneviewer.html		# Ref: https://nvelden.github.io/geneviewer/articles/geneviewer.html
	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
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	selector = ".geneviewer")		selector = ".geneviewer")
	</syntaxhighlight>		</syntaxhighlight>



	=Weblogo=		=Weblogo=

2025-08-01T05:06:01Z

Tree visual with ggtree

← Older revision		Revision as of 05:06, 1 August 2025
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	=Tree visual with ggtree=		=Tree visual with ggtree=
			* Ref book: https://yulab-smu.top/treedata-book/
	<syntaxhighlight lang="sas">		<syntaxhighlight lang="sas">
	setwd("C:/Users/Weigang/Dropbox/Natasha-files/")		setwd("C:/Users/Weigang/Dropbox/Natasha-files/")

2025-05-22T18:12:10Z

Weblogo

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 =Weblogo=
 * install weblogo from [https://github.com/WebLogo/weblogo github]
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 weblogo -f IR4-pep.fas -o ir4-logo.pdf -D fasta -F pdf -A protein -s large -t "IR4" -c chemistry
 </syntaxhighlight>
 =Tree visual with ggtree=
 <syntaxhighlight lang="sas">

2025-05-20T20:12:34Z

multiple regression models (with nested tibble)

← Older revision		Revision as of 20:12, 20 May 2025
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	==multiple regression models (with nested tibble)==		==multiple regression models (with nested tibble)==
	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
			# returns a list of models:
	mods <- test \|>		mods <- test \|>
	group_by(gene_id) \|>		group_by(gene_id) \|>
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	est.ia <- predict(df.mod$models[[1]], newdata = data.frame(mean.val = c(df.boot.mean \|> filter(stat == 'Ia') \|> pull(mean.val))), se.fit = T)		est.ia <- predict(df.mod$models[[1]], newdata = data.frame(mean.val = c(df.boot.mean \|> filter(stat == 'Ia') \|> pull(mean.val))), se.fit = T)

	exp(est.ia$fit)		exp(est.ia$fit)
			exp(est.ia$se.fit)

	~~exp~~(~~est~~.~~ia$se~~.~~fit~~)		# get p vals
			pvals <- lapply(mods$model, \(x) {
			pout <- anova(x)$`Pr(>F)`
			return(list(p.geno = pout[1], p.treat = pout[2], p.int = pout[3]))
			})

			df.pval <- bind_rows(pvals)
	</syntaxhighlight>		</syntaxhighlight>

2025-05-20T19:55:07Z

multiple regression models (with nested tibble)

@@ Line 158: / Line 158: @@
 ==multiple regression models (with nested tibble)==
 <syntaxhighlight lang='bash'>
 # build multiple models, one for each serum:

2025-04-29T22:54:43Z

R tips

← Older revision		Revision as of 22:54, 29 April 2025
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	=R tips=		=R tips=
			==Phylogeny with data==
			* Phylosignal (an alternative to ggtree): https://cran.r-project.org/web/packages/phylosignal/vignettes/Demo_plots.html

	==R one-liners with <code>-e 'EXPR'</code>==		==R one-liners with <code>-e 'EXPR'</code>==
	<syntaxhighlight lang='bash'>		<syntaxhighlight lang='bash'>

2025-04-16T14:24:41Z

R tips

← Older revision		Revision as of 14:24, 16 April 2025
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	=R tips=		=R tips=
	==R one-liners with "-e" EXPR==		==R one-liners with <code>-e 'EXPR'</code>==
	<syntaxhighlight lang='bash'>		<syntaxhighlight lang='bash'>
	# capture numbers in the "tmp" file and then run R:		# capture numbers in the "tmp" file and then run R:

2025-04-16T14:23:52Z

R one-liners

← Older revision		Revision as of 14:23, 16 April 2025
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	=R tips=		=R tips=
	==R one-liners==		==R one-liners with "-e" EXPR==
	<syntaxhighlight lang='bash'>		<syntaxhighlight lang='bash'>
	# capture numbers in the "tmp" file and then run R:		# capture numbers in the "tmp" file and then run R:
	R -e 'mean(scan(file = "tmp")); q()'		R -e 'mean(scan(file = "tmp")); q()'
	</syntaxhighlight>		</syntaxhighlight>

	==Add binomial test with mutate==		==Add binomial test with mutate==
	<syntaxhighlight lang='bash'>		<syntaxhighlight lang='bash'>