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15 results • Page
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Filtering for tag:
outlier
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11
votes
7
replies
5.3k
views
6 follow
Automatic Outlier Detection for RNA-seq data
RNA-Seq
outlier
rrcov
updated 6 days ago by
Melisa
▴ 10 • written 3.4 years ago by
JJ
▴ 560
5
votes
5
replies
489
views
Which of PCA or Heatmap plots are better to exclude outlier replicates from normalised microarray or similar datasets?
microarray
outlier
pca
heatmap
updated 3 months ago by
Mensur Dlakic
★ 10k • written 3 months ago by
Microuser
• 0
1
vote
2
replies
581
views
Detecting Outliers by looking at PCA
RNA-Seq
R
PCA
Outlier
updated 7 months ago by
swbarnes2
9.7k • written 7 months ago by
leekun4
▴ 10
1
vote
5
replies
350
views
How to fix extreme outliers not picked up by DESeq2?
DESeq2
RNA-Seq
Outlier
Cook's Distance
TXImport
updated 7 months ago by
antonioggsousa
★ 2.0k • written 7 months ago by
fisher.w.daniel
• 0
0
votes
0
replies
607
views
angsd Fst outlier
angsd
fst
outlier
manhattan
pvalue
updated 14 months ago by
Biostar
20 • written 15 months ago by
jcolella.jc
• 0
0
votes
2
replies
882
views
LOSITAN only recognising one loci from STACKS genepop file
lositan
outlier
stacks
updated 18 months ago by
a.r.hoelzel
• 0 • written 3.6 years ago by
jamierobertsells
• 0
1
vote
2
replies
727
views
Strange results, in term of DEGs, when including an outlier sample (DEA with DESeq2); someone knows why?
rna-seq
DESeq2
DEA
outlier
2.5 years ago by
fab.sands
• 0
2
votes
4
replies
1.8k
views
how to detect and get genes with outlier expression from RNA-seq
RNA-Seq
outlier
gene expression
updated 2.8 years ago by
h.mon
32k • written 2.8 years ago by
rgescudero
▴ 30
0
votes
3
replies
3.8k
views
Detecting outlier loci from pairwise Fst values
Fst
vcftools
outlier
updated 3.2 years ago by
Shangzhe Zhang
▴ 10 • written 5.9 years ago by
Earendil
▴ 40
0
votes
1
reply
754
views
How meaningful is GO term enrichment of SNP outliers when only a small proportion could be annotated?
GO term enrichment
outliers
SNP
annotation
outlier
3.4 years ago by
belinda-k
• 0
2
votes
4
replies
1.1k
views
Microarray outlier - how to deal? Downweigh? Remove? Re-run everything?
microarray
Illumina-HT12
outlier
limma
qc
updated 3.4 years ago by
Kevin Blighe
72k • written 3.4 years ago by
mismis
• 0
0
votes
2
replies
996
views
Lositan problem with big number of populations
lositan
SNP
outlier
3.5 years ago by
tshmes
▴ 10
0
votes
0
replies
1.6k
views
looking for SNP under selection - is Hardy-Weinberg Equilibrium important?
HWE
bayescan
RADseq
SNP
Outlier
3.6 years ago by
peter
• 0
2
votes
7
replies
1.4k
views
RNAseq continuous variable outliers
rnaseq
deseq2
outlier
continuous
4.8 years ago by
e.antoun
▴ 20
2
votes
7
replies
1.7k
views
Removing contigs with improbable coverage using R?
assembly
coverage
read mapping
statistics
outlier
updated 5.8 years ago by
Michael Dondrup
48k • written 5.8 years ago by
Lesley Sitter
▴ 560
15 results • Page
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Concatenating fasta files based on prefix ?
Concatenating fasta files based on prefix ?
Comment: Concatenating fasta files based on prefix ?
Comment: Concatenating fasta files based on prefix ?
Comment: Concatenating fasta files based on prefix ?
Comment: Concatenating fasta files based on prefix ?
Comment: Bioinformatics startup market analysis
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Comment: Bioinformatics startup market analysis
by
gtechbio
▴ 20
Dear @grant.hovhannisyan, thank you for the advice. In fact we are already in touch with two local genomics facilities, though as you have …
Answer: No annotation peaks when running homer
by
geneticatt
▴ 110
Try raising your p-value to make sure that they aren't all just being filtered out by that threshold (which seems pretty low).
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴ 40
It looks like the following: system(paste0("mafft --anysymbol --maxiterate 1000 Alignment_output/",GENE,".fa > ",GENE,".mafft.fa")) GE…
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴ 40
Yes, I am using the following loop first in R to process all the files. This is the code that I am running first: blastn.filelist <- s…
Comment: Bioinformatics startup market analysis
by
grant.hovhannisyan
★ 2.1k
agreed, especially if no private information (names, clinical status, etc) is needed, this information should be freely accessible.
Comment: question when using topgo
by
Kevin Blighe
72k
^^ this
Answer: question when using topgo
by
seidel
7.6k
The GenTable() function has a parameter called *numChar* that controls this: "the GO term definition will be truncated such that only the f…
Comment: why my volcano plot looks strange?
by
cpad0112
15k
is it `log10p` or `-log10p` on y-axis?
Answer: How to get GO terms to specific to perticular biological process
by
geneticatt
▴ 110
See the 'is_a' field in the go.obo file. If you're looking for all subcategories of GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl…
Comment: How to perform multiple alignment using MAFFT?
by
Dunois
▴ 620
What does your `system()` command look like now, after having added `--anysymbol`? I am guessing you added `--anysymbol` right before that …
Comment: How to perform multiple alignment using MAFFT?
by
Ram
32k
Are you using this statement in a loop? If so, please refine your command to error out with the file that produces the error - maybe print …
Answer: How to obtain FDR across all regions investigated in DiffBind
by
Rory Stark
★ 1.0k
The "correct" way to retrieve results in `DiffBind` is via the `dba.report()` function. Setting `th=1` returns all results with FDR <= 1.0,…
Comment: Batch effect correction of 2 studies with different covariates
by
Dunois
▴ 620
If you run `RUVseq` on the data from study B only, you'd get predicted values for age and sex but these will be numerical. I suppose you co…
Comment: How to find single copy family from InParanoid output
by
Dunois
▴ 620
I'd just use [`OrthoFinder`][1]. It outputs a separate directory of single copy orthologs if any such (ortho)groups exist in your data set.…
Comment: Concatenating fasta files based on prefix ?
by
seidel
7.6k
Play with the components of the solution @5heikki gave you to troubleshoot and learn. Are you familiar with loops and pipes? The first part…
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