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120,976 results • Page
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0
votes
1
reply
142
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What is the best way to know if a pair of genes is random?
terms
genes
go
updated 6 minutes ago by
shelkmike
★ 1.5k • written 3 days ago by
Ana
• 0
0
votes
1
reply
129
views
How to save the AlphaFold PAE plot as an image in ChimeraX using command line ?
PAE
ChimeraX
AlphaFold
updated 39 minutes ago by
LauferVA
4.7k • written 2 days ago by
Picasa
▴ 670
4
votes
8
replies
645
views
Extract length of sample sequence from vcf
microsatellites
bcftools
vcf
indels
variants
4 hours ago by
jahnreinhard.ringger
• 0
1
vote
0
replies
33
views
News:
Building an mmCIF parser for enzyme structure analysis — feedback & ideas welcome!
mmcif
updated 1 hour ago by
GenoMax
150k • written 4 hours ago by
Shravya
• 0
1
vote
0
replies
39
views
News:
LAST CALL - Bioinformatics Pipeline Development with Nextflow - May 19-21, 2025 (online) - Apply Now
nextflow
rnaseq
workshop
4 hours ago by
ecSeq Bioinformatics
▴ 20
0
votes
1
reply
116
views
RNA-seq, three comparisons - stick to one linear model, or use separate models?
statistics
mixed_effect_model
linear_model
stats
RNAseq
updated 5 hours ago by
ATpoint
87k • written 18 hours ago by
noodlejackson
▴ 40
836
votes
167
replies
173k
views
111 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 1 day ago by
Biostar
3.4k • written 8.4 years ago by
Istvan Albert
102k
0
votes
1
reply
70
views
Using Principal Components may muddle the detecting power of a GWAS?
q-value
covariates
genomic-inflation
pca
gwas
updated 5 hours ago by
DBScan
▴ 470 • written 7 hours ago by
AndrMod
• 0
0
votes
0
replies
50
views
Use Seed or Full Alignments from Pfam HMM as a filter step
hmm
sequences
metagenomic
7 hours ago by
Janelyn123
• 0
0
votes
2
replies
129
views
Helicobacter pylori low-rate alignment
bioinformatics
transcriptomics
RNA-seq
updated 1 hour ago by
GenoMax
150k • written 23 hours ago by
Ariadna
▴ 20
14
votes
3
replies
11k
views
Can The Wget Command Be Used To Download Pdbs
pdb
updated 8 hours ago by
Calvin
• 0 • written 13.5 years ago by
Harpalss
▴ 310
0
votes
3
replies
231
views
Is a log2 transformation an essential step in preparing expression data for machine learning?
Machinelearning
microarray
preproccessing
updated 19 hours ago by
Mensur Dlakic
★ 29k • written 1 day ago by
Sib
▴ 60
0
votes
2
replies
827
views
How to re-annotate the structure of gene against a known genomic file
RNA-Seq
updated 20 hours ago by
Mensur Dlakic
★ 29k • written 5.9 years ago by
Kanoo
• 0
0
votes
1
reply
159
views
ONT Live-Basecalling Issue?
ONT
minKNOW
live-basecalling
updated 19 hours ago by
GenoMax
150k • written 1 day ago by
Akshay
• 0
2
votes
4
replies
200
views
Identify gene from sequence at scale in non-model organisms
name
sequence
gene
updated 23 hours ago by
shelkmike
★ 1.5k • written 1 day ago by
matthewmerkin32
• 0
0
votes
0
replies
111
views
News:
Cellosaurus release 52 is available
database
line
cell
knowledgebase
biocuration
1 day ago by
Amos Bairoch
▴ 130
0
votes
2
replies
235
views
WGCNA
problem
updated 1 day ago by
GenoMax
150k • written 3 days ago by
香
• 0
0
votes
0
replies
215
views
Seeking Advice on Causal Inference for Treatment Effect Prediction (Small Sample, Genomic Covariates)
inference
causal
2 days ago by
oghzzang
▴ 50
5
votes
5
replies
408
views
Batch effect
RNAseq
Batch-Effect
1 day ago by
Fatemeh
▴ 40
0
votes
4
replies
347
views
convert Gene ID to Gene Symbol
gene-id
updated 2 days ago by
pinheirofabiano
▴ 110 • written 4 days ago by
majorprogeria
• 0
0
votes
4
replies
269
views
TPM vs FPKM divergence at high values
tpm
fpkm
normalisation
updated 1 day ago by
ATpoint
87k • written 2 days ago by
megancgrdnr
• 0
0
votes
1
reply
191
views
Blastx issue
Long
coding
non
blastx
RNA
updated 2 days ago by
JustinZhang
▴ 130 • written 2 days ago by
Avik
• 0
0
votes
1
reply
177
views
News:
Structural bioinformatics workshop
Structural
bioinformatics
updated 2 days ago by
GenoMax
150k • written 2 days ago by
reetesh
• 0
1
vote
10
replies
518
views
How to test the similarity of two gene expression profiles
test
gene
sets
updated 2 days ago by
JustinZhang
▴ 130 • written 3 days ago by
htchd
• 0
3
votes
3
replies
212
views
Which are the different kinds of GeneID that exist?
R
RNA-Seq
2 days ago by
pinheirofabiano
▴ 110
0
votes
0
replies
129
views
Error using DWLS
deconvolution
DWLS
RNAseq
3 days ago by
Ana
• 0
0
votes
5
replies
1.7k
views
How to remove this module selection error?
WGCNA
updated 3 days ago by
香
• 0 • written 2.3 years ago by
gupta00aritra
• 0
0
votes
1
reply
791
views
bbsplit : How to configure ambiguous/ambiguous2 parameters in order to consider as unmapped reads, reads mapped on both human/mouse references.
bbsplit
nextflow
updated 2 days ago by
GenoMax
150k • written 3 days ago by
ZheFrench
▴ 590
1
vote
2
replies
200
views
Limma for DEG aalysis
R
DEG
limma
ANALYSIS
3 days ago by
rahma.khoualdia
• 0
0
votes
0
replies
161
views
deletion impact
vcf
updated 3 days ago by
GenoMax
150k • written 3 days ago by
HarperReed
• 0
0
votes
2
replies
213
views
Help finding GTEx v8 file
GTEx
SHAPEIT2
2 days ago by
蒲蒲
• 0
2
votes
5
replies
266
views
Idat file processing issue with command line cli
CanineHTS
IDAT
2 days ago by
1769mkc
★ 1.2k
0
votes
0
replies
134
views
is there a way to get --ref paths to prioritize my order with vg call?
call
vgcall
3 days ago by
PolenP
• 0
0
votes
1
reply
193
views
Has anyone tried used simple ML models to identify virulence genes?
genetics
R
classifier
genomics
machinelearning
updated 3 days ago by
Mensur Dlakic
★ 29k • written 3 days ago by
Jack
• 0
0
votes
4
replies
273
views
What does vg autoindex mpmap do?
vg
mpmap
autoindex
20 minutes ago by
Ziyue
• 0
3
votes
4
replies
345
views
How to keep the same view for different AlphaFold 3 simulations in ChimeraX?
chimerax
alphafold
3
updated 2 days ago by
LauferVA
4.7k • written 3 days ago by
Picasa
▴ 670
0
votes
0
replies
153
views
filtering genes before or after the correlation?
co-expression
feature
selection
correlation
3 days ago by
tyasird
▴ 10
0
votes
16
replies
703
views
Which tools use or rely on the XA tag in SAM/BAM/CRAM files?
cram
XA
compress
updated 2 days ago by
JustinZhang
▴ 130 • written 5 days ago by
Maarten
• 0
2
votes
4
replies
268
views
Which additional files are needed for the -taxids option in blast?
decontamination
taxids
blastn
updated 3 days ago by
GenoMax
150k • written 3 days ago by
WaspInSpace
• 0
0
votes
0
replies
168
views
Job:
Assistant, Associate, or Full Project Scientist in Neurobiology
Biology
Neuroscience
Neurobiology
3 days ago by
UCSDBioSci
▴ 30
1
vote
3
replies
285
views
Is Centering and Scaling Essential for Expression Data as Input for Machine Learning Algorithms?
featureselection
microarray
preprocessing
1 day ago by
Sib
▴ 60
0
votes
0
replies
180
views
News:
Online Course: Machine learning for multi-omics integration (9–11 June)
Machine-Learning
Mult-Omics
4 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
255
views
Single Nuclei RNA-Sequencing Analysis Without CellRanger
CellRanger
single-cell
snRNA-seq
2 days ago by
16_masques.vole
• 0
0
votes
0
replies
183
views
Demultiplexing samples when barcodes repeat: Any advice?
seurat
demultiplex
singlecell
scRNAseq
4 days ago by
tia
• 0
1
vote
1
reply
290
views
Unable to generate hierarchical and circle plot using CellChat
cellchat
scRNAseq
Seurat
4 days ago by
S
• 0
0
votes
8
replies
552
views
Discrepancy between positions on IGV and NCBI's PrimerBLAST
igv
primer
blast
3 days ago by
Rozita
▴ 40
0
votes
2
replies
266
views
Steps for meta-analysis
Meta-Analysis
differential-expression
updated 3 days ago by
Ram
45k • written 4 days ago by
majorprogeria
• 0
5
votes
1
reply
280
views
News:
The IGB team needs your help! Write a letter of support to keep the Integrated Genome Browser running!
IGB
Integrated-Genome-Browser
Funding
updated 4 days ago by
microfuge
★ 2.0k • written 4 days ago by
Nowlan Freese
▴ 900
0
votes
0
replies
217
views
how pd tag were defined in gaf file
vg
4 days ago by
chuanj8848
• 0
4
votes
2
replies
331
views
SRA Toolkit - three fastq files - which is which?
scrna
sratoolkit
updated 4 days ago by
GenoMax
150k • written 4 days ago by
Neat
• 0
120,976 results • Page
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Are there any software packages available to calculate ploidy from RNA-Seq data?
Answer: vg autoindex seems stuck after a week of running
vg autoindex seems stuck after a week of running
Comment: Identify gene from sequence at scale in non-model organisms
LAST CALL - Bioinformatics Pipeline Development with Nextflow - May 19-21, 2025 (online) - Apply Now
A: why A/T or C/G are ambiguous SNPs?
Future of Microarrays
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Recent Replies
Answer: What is the best way to know if a pair of genes is random?
by
shelkmike
★ 1.5k
I don't know about the best way, but one method to do this, I think, could look as follows:<br> 1) Take all possible pairs of genes and fo…
Comment: What does vg autoindex mpmap do?
by
Ziyue
• 0
I increased the temp dir size limit to 4 TB by adding `--gcsa-size-limit 4398046511104` ``` Elapsed: 2 days, 19 hours, 18 minutes, 21 seco…
Answer: How to save the AlphaFold PAE plot as an image in ChimeraX using command line ?
by
LauferVA
4.7k
First, to all, see also the main thread & comments section of this related post: https://www.biostars.org/p/9611169/#9611243. Hi @picasa …
Comment: Identify gene from sequence at scale in non-model organisms
by
matthewmerkin32
• 0
Yep, it was just down earlier but I managed to get the local installation to work anyway, so thanks for the great suggestion.
Comment: Identify gene from sequence at scale in non-model organisms
by
shelkmike
★ 1.5k
I've just tried the link and it works.
Comment: Helicobacter pylori low-rate alignment
by
GenoMax
150k
> They likely have a read length of about 400bp Looks like the data is ~130 bp.
Answer: Extract length of sample sequence from vcf
by
jahnreinhard.ringger
• 0
I have figured out the issue, and also unfortunately why counting with awk will not work, but I do not have a solution to my problem. Th…
Comment: Using Principal Components may muddle the detecting power of a GWAS?
by
DBScan
▴ 470
If you are doing PCA to capture population stratification, you should not perform PCA only on your data, but project your samples onto a pr…
Answer: RNA-seq, three comparisons - stick to one linear model, or use separate models?
by
ATpoint
87k
There is no scrict rule for this. Generally, if variability between groups is somewhat in the same ballpark, e.g. approxiated by PCA, then …
Comment: Identify gene from sequence at scale in non-model organisms
by
matthewmerkin32
• 0
Thanks for the suggestion, I had not heard of PANNZER. However, when I click on the link given in their paper (http://ekhidna2.biocenter.he…
Answer: Helicobacter pylori low-rate alignment
by
colindaven
7.4k
These are really really old 454 data. They likely have a read length of about 400bp. The bowtie2 aligner is not suitable for these AFAIK. …
Comment: Can The Wget Command Be Used To Download Pdbs
by
Calvin
• 0
The URL of the PDB website has been changed, you can still download PDB files directly through URLs such as : http://www.rcsb.org/pdb/file…
Comment: ONT Live-Basecalling Issue?
by
GenoMax
150k
Did this block eliminate itself over time? It looks like ~4 M initial reads in your run are in "paused" state. Have not heard of this happe…
Answer: Is a log2 transformation an essential step in preparing expression data for mach
by
Mensur Dlakic
★ 29k
> Is a log2 transformation an essential step in preparing the expression data for machine learning, or can the normalized raw expression da…
Comment: How to re-annotate the structure of gene against a known genomic file
by
Mensur Dlakic
★ 29k
If you look above from this writing, this question was asked 5.9 years ago. If you click on user's name, you will see that they last visite…
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