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16 results • Page
1 of 1
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Votes
Replies
0
votes
0
replies
17
views
PCA plot
DESeq2
PCAplot
2 hours ago by
Aaliya
▴ 10
0
votes
0
replies
44
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
4 hours ago by
4fzcgueyp5
• 0
0
votes
1
reply
94
views
Annovar using R package
Annovar
gnomAD
R
updated 6 hours ago by
Pierre Lindenbaum
161k • written 9 hours ago by
DKA
▴ 40
0
votes
0
replies
55
views
Finding orthologs between genome error
OMA
OMAbrowser
12 hours ago by
hemantcnaik
• 0
0
votes
0
replies
72
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 10 hours ago by
Ram
43k • written 15 hours ago by
glaciya2018
• 0
0
votes
0
replies
111
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
15 hours ago by
pramach1
▴ 40
0
votes
1
reply
100
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 13 hours ago by
Sofia
• 0 • written 17 hours ago by
mawigoj318
• 0
0
votes
0
replies
82
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
19 hours ago by
salias
• 0
0
votes
2
replies
146
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 10 hours ago by
Ram
43k • written 20 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
74
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 10 hours ago by
Ram
43k • written 20 hours ago by
newuser2024
• 0
0
votes
1
reply
111
views
alignment result
RNA-seq
samtools
hisat2
updated 10 hours ago by
Ram
43k • written 21 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
65
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 10 hours ago by
Ram
43k • written 23 hours ago by
Jeyong
• 0
0
votes
2
replies
200
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 10 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
0
votes
5
replies
273
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
18 hours ago by
njornet
▴ 20
2
votes
4
replies
238
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
21 hours ago by
samuelkalandarov2002
▴ 10
0
votes
6
replies
423
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 20 hours ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
16 results • Page
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Recent Votes
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
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Recent Awards •
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Popular Question
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camillab.
▴ 160
Popular Question
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Simone
▴ 10
Popular Question
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carlopecoraro2
★ 2.5k
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daffodil
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Russ
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Adyasha
• 0
Recent Replies
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
Answer: Network Alignment
by
Scooter
▴ 280
Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…
Answer: How could I generate a gi_taxid_nucl.dmp file similar to the one previously host
by
ZhangYuanfeng
• 0
JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…
Comment: PCA plot (Suggestions Needed)
by
Aaliya
▴ 10
I have actually used DESeq2 data.
Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
by
Dateline
• 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
Answer: Heatmap and rna-seq
by
Kevin Blighe
87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies
by
Kevin Blighe
87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
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