make.file(inputdir=MiSeq_SOP, type=fastq, prefix=stability)
summary.qs(im.contigs.fasta)
screen.qs(im.contigs.fasta, ups, maxambig=0, maxlength=275)
或者screen.qs(im.contigs.fasta, ups, im.contigs.summary, maxambig=0, maxlength=275)
summary.qs(d.fasta)
中国武术散打unique.qs(d.fasta)
count.qs(d.names, ups)
summary.qs(d.count_table)
pcr.qs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F, processors=4)
rename.file(input=silva.bacteria.pcr.fasta, new=silva.v4.fasta)
summary.qs(fasta=silva.v4.fasta)
align.qs(d.unique.fasta, reference=silva.v4.fasta)
summary.qs(d.unique.align, d.count_table)
screen.qs(d.unique.align, d.count_table, d.unique.summary, start=1968, end=11550, maxhomop=8)
summary.qs(fasta=current, count=current)
filter.qs(d.align, vertical=T, trump=.)
unique.qs(d.filter.fasta, unt_table)
pre.cluster(d.filter.unique.fasta, unt_table, diffs=2)
chimera.varch(d.filter.unique.precluster.fasta, d.filter.unt_table, dereplicate=t)
remove.qs(d.filter.unique.precluster.fasta, d.filter.unique.precluster.denovo.varch.accnos)
summary.qs(fasta=current, count=current)
classify.qs(d.filter.unique.precluster.pick.fasta, d.filter.unique.precluster.denovo.unt_table, reference=traint9_032012.pds.fasta, taxonomy=traint9_032012.pds.tax, cutoff=80)
remove.lineage(d.filter.unique.precluster.pick.fasta, d.filter.unique.precluster.denovo.unt_table, d.filter.unique.precluster.pick.pds.wang.taxonomy, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota)
手几
summary.tax(taxonomy=current, count=current)
ilter.unique.precluster.pick.pick.fasta, groups=Mock)梦见自己的孩子死了是什么意思
<(d.filter.unique.precluster.pick.pick.pick.fasta, d.filter.unique.precluster.denovo.varch.pick.unt_table, reference=HMP_MOCK.v35.fasta, aligned=F)
dist.qs(d.filter.unique.precluster.pick.pick.pick.fasta, cutoff=0.03)
cluster(d.filter.unique.precluster.pick.pick.pick.dist, d.filter.unique.precluster.denovo.varch.pick.unt_table)
make.shared(d.filter.unique.precluster.pick.pick.pick.opti_mcc.list,d.filter.unique.precluster.denovo.varch.pick.unt_table,label=0.03)
rarefaction.single(d.filter.unique.precluster.pick.pick.pick.opti_mcc.shared)
范巴斯滕
dist.qs(d.filter.unique.precluster.pick.pick.pick.fasta, cutoff=0.03)
cluster(d.filter.unique.precluster.pick.pick.pick.dist,d.filter.unique.precluster.denovo.varch.pick.unt_table)
cluster.split(d.filter.unique.precluster.pick.pick.pick.fasta,d.filter.unique.precluster.denovo.varch.pick.unt_table,d.filter.unique.precluster.pick.pds.wang.pick.pick.taxonomy,splitmethod=classify, taxlevel=4, cutoff=0.03)
make.shared(d.filter.unique.precluster.pick.pick.pick.opti_mcc.unique_list.list,d.filter.unique.precluster.denovo.varch.pick.unt_table,label=0.03)
phylotype(d.filter.unique.precluster.pick.pds.wang.pick.pick.taxonomy)
make.shared(d.filter.unique.precluster.pick.pds.wang.list,d.filter.unique.precluster.denovo.varch.pick.pick新中式实木沙发
.unt_table,label=1)
dist.qs(d.filter.unique.precluster.pick.pick.pick.fasta,output=lt,processors=4)
clearcut(d.filter.unique.precluster.pick.pick.pick.phylip.dist)
rename.file(d.filter.unique.precluster.denovo.varch.pick.unt_table,d.filter.unique.precluster.pick.pick.,d.filter.unique.precluster.pick.pick.pick.opti_mcc.shared,d.filter.unique.precluster.pick.pick.pick.opti_mcc.s.taxonomy)
中国地理位置
sub.sample(shared=stability.opti_mcc.shared, size=2392)
rarefaction.single(shared=stability.opti_mcc.shared, calc=sobs, freq=100)
summary.single(shared=stability.opti_mcc.shared, calc=nqs-coverage-sobs-invsimpson, subsample=2392)
heatmap.bin(shared=stability.opti_mcc.0.03.subsample.shared, scale=log2, numotu=50)
dist.shared(shared=stability.opti_mcc.shared, calc=thetayc-jclass, subsample=2392)（这一步出现错误，不能继续运行这个命令，终端显示：You have not provided enough vaild groups. I cannot run th
e command.）
heatmap.sim(phylip=stability.opti_mcc.thetayc.0.03.lt.ave.dist)
heatmap.sim(phylip=stability.opti_mcc.jclass.0.03.lt.ave.dist)
venn(shared=stability.opti_mcc.0.03.subsample.shared, groups=F3D0-F3D1-F3D2-F3D3)
tree.shared(phylip=stability.opti_mcc.thetayc.0.03.lt.ave.dist)
parsimony(tree=stability.opti_mcc.thetayc.0.03., group=mou.time.design, groups=all)
pcoa(phylip=stability.opti_mcc.thetayc.0.03.lt.ave.dist)
nmds(phylip=stability.opti_mcc.thetayc.0.03.lt.ave.dist)
nmds(phylip=stability.opti_mcc.thetayc.0.03.lt.ave.dist, mindim=3, maxdim=3)
amova(phylip=stability.opti_mcc.thetayc.0.03.lt.ave.dist, design=mou.time.design)
homova(phylip=stability.opti_mcc.thetayc.0.03.lt.ave.dist, design=mou.time.design)
遇见未知的自己读后感
corr.axes(axes=stability.opti_mcc.thetayc.0.03.lt.ave.pcoa.axes, shared=stability.opti_mcc.0.03.subsample.shared, method=spearman, numaxes=3)
corr.axes(axes=stability.opti_mcc.thetayc.0.03.lt.ave.pcoa.axes, metadata=adata, method=spearman, numaxes=3)
mancan
metastats(shared=stability.opti_mcc.0.03.subsample.shared, design=mou.time.design)
lef(shared=stability.opti_mcc.0.03.subsample.shared, design=mou.time.design)
phylo.diversity(, count=stability
.count_table, rarefy=T)
unifrac.unweighted(, unt_table, distance=lt, processors=2, random=F, subsample=2392)
unifrac.weighted(, unt_table, distance=lt, processors=2, random=F, subsample=2392)
