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80 results • Page
2 of 2
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Views
Votes
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0
votes
1
reply
133
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 1 day ago by
dthorbur
★ 2.0k • written 1 day ago by
Umer
▴ 50
1
vote
1
reply
129
views
constructing pangenome through psvcp
psvcp
pangenome
7 hours ago by
analyst
▴ 50
0
votes
0
replies
125
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
2 days ago by
ebertomeup
• 0
0
votes
0
replies
124
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 5 days ago by
Ram
43k • written 19 days ago by
atharvakarkare14
▴ 40
0
votes
0
replies
119
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
2 days ago by
Jsarria.EEAD
• 0
0
votes
0
replies
119
views
cat-bgen fail
bgenix
updated 2 days ago by
Ram
43k • written 2 days ago by
lambard
• 0
0
votes
0
replies
114
views
Use of ichor CNA
Dog
CNA
genome
2 days ago by
sainavyav22
• 0
0
votes
0
replies
113
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Rodolfo Adrián
• 0
0
votes
0
replies
112
views
lncRNA
tcga
lncrna
5 days ago by
jain72744
▴ 10
0
votes
0
replies
110
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
3 days ago by
jway
• 0
0
votes
0
replies
110
views
Is there a real ground truth for CNV data?
CNV
4 days ago by
jennyp0706
• 0
0
votes
0
replies
109
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
1 day ago by
O.rka
▴ 720
0
votes
0
replies
105
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
5 days ago by
atariw
▴ 10
0
votes
0
replies
105
views
reference-free assembly error assessment tools
assembly
5 days ago by
lagartija
▴ 160
0
votes
0
replies
104
views
Reference panel of normals for ensembl named refgenome
Mutect2
5 days ago by
gernophil
▴ 80
0
votes
0
replies
102
views
genomic region of transcription factor
search
HOMER
motif
1 day ago by
qudrat.nii
▴ 10
0
votes
0
replies
99
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Dude
• 0
1
vote
0
replies
98
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
5 days ago by
tomas4482
▴ 400
0
votes
0
replies
96
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
3 days ago by
brunofelicianodeomena
• 0
0
votes
0
replies
95
views
ReactomeGSA
ReactomeGSA
3 days ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
94
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
4 days ago by
Spring
• 0
0
votes
0
replies
90
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
1 day ago by
Varsha
• 0
0
votes
0
replies
88
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
5 days ago by
JACKY
▴ 140
0
votes
0
replies
88
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 1 day ago by
GenoMax
142k • written 1 day ago by
yura.grabovska
▴ 90
0
votes
0
replies
82
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Long
• 0
0
votes
1
reply
82
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 10 hours ago by
ATpoint
82k • written 11 hours ago by
Jacek
▴ 20
0
votes
0
replies
78
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
1 day ago by
kilcdincer
▴ 10
0
votes
0
replies
69
views
How can i use ESM-1v ?
VEP
ESM-1v
20 hours ago by
Meto
• 0
0
votes
0
replies
58
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
9 hours ago by
Moinuddin
• 0
0
votes
0
replies
43
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 6 hours ago by
Pierre Lindenbaum
161k • written 6 hours ago by
Mohamed Samir
▴ 20
80 results • Page
2 of 2
Recent Votes
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
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Recent Replies
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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