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16 results • Page
1 of 1
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49
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How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
6 hours ago by
rohitsatyam102
▴ 850
1
vote
2
replies
184
views
alignment result
RNA-seq
samtools
hisat2
16 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
58
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
13 hours ago by
Aspire
▴ 300
0
votes
5
replies
263
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 9 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
0
votes
1
reply
130
views
PCA plot
DESeq2
PCAplot
updated 8 hours ago by
jkim
▴ 170 • written 19 hours ago by
Aaliya
▴ 10
0
votes
1
reply
376
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 7 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
43
views
how to read graph_test output of monocle 3
monocle3
6 hours ago by
synat.keam
▴ 100
0
votes
0
replies
38
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
5 hours ago by
Emily
▴ 10
0
votes
0
replies
45
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
5 hours ago by
avocado123
• 0
0
votes
1
reply
56
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 2 hours ago by
ATpoint
82k • written 3 hours ago by
AaronJaime
• 0
0
votes
2
replies
140
views
Highest variable features in single cell data
single-cell
updated 2 hours ago by
Ram
43k • written 15 hours ago by
Kazo
• 0
0
votes
2
replies
157
views
Annovar using R package
Annovar
gnomAD
R
2 hours ago by
DKA
▴ 40
0
votes
0
replies
18
views
Designing single-stable RNA molecules
structure
RNA
1 hour ago by
Edna
• 0
0
votes
0
replies
86
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
21 hours ago by
4fzcgueyp5
• 0
0
votes
0
replies
22
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
1 hour ago by
simplitia
▴ 130
0
votes
4
replies
238
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
14 hours ago by
sehriban.buyukkilic
▴ 10
16 results • Page
1 of 1
Recent Votes
Comment: Sequence read length shorter than flow cell specification
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
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82k
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zdiazmar
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Recent Replies
Answer: Rare Disease Variant Pathway Analysis
by
LauferVA
4.2k
Hi @efc1e545 , First a caveat. the information we most need in order to help guide you to a successful conclusion is not provided in thi…
Answer: Sequence read length shorter than flow cell specification
by
swbarnes2
14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package
by
DKA
▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
ATpoint
82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
by
ATpoint
82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
kilcdincer
▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases
by
GenoMax
141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases
by
5heikki
11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work?
by
Bioinfotec
▴ 10
I think when you give indent to seuObj : ```r Idents(seuObj) <- 'RNA_snn_res.0.1' ``` You may wrongly assign other value to it such as `…
Answer: ScRNAseq-How to correctly choose cell type marker genes
by
Bioinfotec
▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question
by
Bioinfotec
▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification
by
GenoMax
141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing
by
rohitsatyam102
▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
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