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120,974 results • Page
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0
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10
views
Using Principal Components may muddle the detecting power of a GWAS?
q-value
covariates
genomic-inflation
pca
gwas
21 minutes ago by
AndrMod
• 0
0
votes
0
replies
14
views
Use Seed or Full Alignments from Pfam HMM as a filter step
hmm
sequences
metagenomic
40 minutes ago by
Janelyn123
• 0
0
votes
1
reply
80
views
Helicobacter pylori low-rate alignment
bioinformatics
transcriptomics
RNA-seq
updated 52 minutes ago by
colindaven
7.4k • written 16 hours ago by
Ariadna
▴ 20
14
votes
3
replies
10k
views
Can The Wget Command Be Used To Download Pdbs
pdb
updated 1 hour ago by
Calvin
• 0 • written 13.5 years ago by
Harpalss
▴ 310
0
votes
0
replies
63
views
RNA-seq, three comparisons - stick to one linear model, or use separate models?
statistics
mixed_effect_model
linear_model
stats
RNAseq
11 hours ago by
noodlejackson
▴ 40
0
votes
3
replies
202
views
Is a log2 transformation an essential step in preparing expression data for machine learning?
Machinelearning
microarray
preproccessing
updated 13 hours ago by
Mensur Dlakic
★ 29k • written 1 day ago by
Sib
▴ 60
0
votes
2
replies
803
views
How to re-annotate the structure of gene against a known genomic file
RNA-Seq
updated 13 hours ago by
Mensur Dlakic
★ 29k • written 5.9 years ago by
Kanoo
• 0
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
145
views
ONT Live-Basecalling Issue?
ONT
minKNOW
live-basecalling
updated 12 hours ago by
GenoMax
150k • written 1 day ago by
Akshay
• 0
1
vote
2
replies
149
views
Identify gene from sequence at scale in non-model organisms
name
sequence
gene
8 minutes ago by
matthewmerkin32
• 0
0
votes
0
replies
94
views
News:
Cellosaurus release 52 is available
database
line
cell
knowledgebase
biocuration
1 day ago by
Amos Bairoch
▴ 130
0
votes
2
replies
219
views
WGCNA
problem
updated 1 day ago by
GenoMax
150k • written 2 days ago by
香
• 0
0
votes
0
replies
196
views
Seeking Advice on Causal Inference for Treatment Effect Prediction (Small Sample, Genomic Covariates)
inference
causal
1 day ago by
oghzzang
▴ 50
0
votes
0
replies
106
views
How to save the AlphaFold PAE plot as an image in ChimeraX using command line ?
PAE
ChimeraX
AlphaFold
1 day ago by
Picasa
▴ 670
5
votes
5
replies
387
views
Batch effect
RNAseq
Batch-Effect
19 hours ago by
Fatemeh
▴ 40
0
votes
4
replies
330
views
convert Gene ID to Gene Symbol
gene-id
updated 1 day ago by
pinheirofabiano
▴ 110 • written 4 days ago by
majorprogeria
• 0
0
votes
4
replies
247
views
TPM vs FPKM divergence at high values
tpm
fpkm
normalisation
updated 19 hours ago by
ATpoint
87k • written 2 days ago by
megancgrdnr
• 0
0
votes
1
reply
179
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
167
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
501
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
201
views
Which are the different kinds of GeneID that exist?
R
RNA-Seq
2 days ago by
pinheirofabiano
▴ 110
0
votes
0
replies
120
views
Error using DWLS
deconvolution
DWLS
RNAseq
2 days ago by
Ana
• 0
0
votes
5
replies
1.7k
views
How to remove this module selection error?
WGCNA
updated 2 days ago by
香
• 0 • written 2.3 years ago by
gupta00aritra
• 0
0
votes
1
reply
712
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 2 days ago by
ZheFrench
▴ 590
1
vote
2
replies
185
views
Limma for DEG aalysis
R
DEG
limma
ANALYSIS
2 days ago by
rahma.khoualdia
• 0
0
votes
0
replies
147
views
deletion impact
vcf
updated 2 days ago by
GenoMax
150k • written 2 days ago by
HarperReed
• 0
0
votes
2
replies
199
views
Help finding GTEx v8 file
GTEx
SHAPEIT2
2 days ago by
蒲蒲
• 0
2
votes
5
replies
255
views
Idat file processing issue with command line cli
CanineHTS
IDAT
2 days ago by
1769mkc
★ 1.2k
0
votes
0
replies
126
views
What is the best way to know if a pair of genes is random?
terms
genes
go
2 days ago by
Ana
• 0
0
votes
0
replies
126
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
185
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
3
replies
257
views
What does vg autoindex mpmap do?
vg
mpmap
autoindex
updated 1 day ago by
Jordan M Eizenga
▴ 690 • written 3 days ago by
Ziyue
• 0
3
votes
4
replies
328
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
143
views
filtering genes before or after the correlation?
co-expression
feature
selection
correlation
3 days ago by
tyasird
▴ 10
0
votes
16
replies
677
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 4 days ago by
Maarten
• 0
2
votes
4
replies
256
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
160
views
Job:
Assistant, Associate, or Full Project Scientist in Neurobiology
Biology
Neuroscience
Neurobiology
3 days ago by
UCSDBioSci
▴ 30
1
vote
3
replies
273
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
172
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
247
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
174
views
Demultiplexing samples when barcodes repeat: Any advice?
seurat
demultiplex
singlecell
scRNAseq
4 days ago by
tia
• 0
1
vote
1
reply
280
views
Unable to generate hierarchical and circle plot using CellChat
cellchat
scRNAseq
Seurat
4 days ago by
S
• 0
0
votes
8
replies
540
views
Discrepancy between positions on IGV and NCBI's PrimerBLAST
igv
primer
blast
2 days ago by
Rozita
▴ 40
0
votes
2
replies
253
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
271
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
208
views
how pd tag were defined in gaf file
vg
4 days ago by
chuanj8848
• 0
4
votes
2
replies
318
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
0
votes
0
replies
171
views
Using DEXseq on kallisto tsv outputs ?
alignement
DEXseq
kallisto
4 days ago by
Gerard
▴ 10
1
vote
0
replies
205
views
Herald:
The Biostar Herald for Wednesday, April 09, 2025
herald
4 days ago by
Biostar
3.4k
6
votes
6
replies
489
views
Methods for directional pathway analysis of DEGs?
Pathway-analysis
ORA
GSEA
Limma
updated 4 days ago by
Gordon Smyth
★ 7.9k • written 6 days ago by
Steven
▴ 10
120,974 results • Page
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Comment: Identify gene from sequence at scale in non-model organisms
Answer: JASPAR2024_getMatrixSet error
A: Can The Wget Command Be Used To Download Pdbs
Still confused about exons versus CDS
Answer: Still confused about exons versus CDS
Answer: Still confused about exons versus CDS
A: Annotatepeaks Function From Homer
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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. …
Answer: 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…
Comment: Is a log2 transformation an essential step in preparing expression data for mach
by
Sib
▴ 60
I would greatly appreciate it if you could refer me to a tutorial on conducting feature selection for microarray data using some (or all) o…
Comment: Identify gene from sequence at scale in non-model organisms
by
shelkmike
★ 1.5k
I don't understand why you think that you need some gene names to perform GO annotation. Just upload your proteins to PANNZER. It is an onl…
Comment: How to re-annotate the structure of gene against a known genomic file
by
Olayemi F.
• 0
Hey Kanoo, How did this later turn out for you?
Comment: Batch effect
by
Fatemeh
▴ 40
Thanks very much.
Comment: Is a log2 transformation an essential step in preparing expression data for mach
by
ATpoint
87k
You're shooting buzz words as in the question before. Please read the underlying literature and follow guided tutorials. There is no genera…
Comment: TPM vs FPKM divergence at high values
by
ATpoint
87k
Please show the functions to calculate this. Both transformations are simple division and multiplication operations with the column sums of…
Comment: Is Centering and Scaling Essential for Expression Data as Input for Machine Lear
by
Sib
▴ 60
Sorry, is log2 taransformation also needed? Or we can apply ML methods on expression data without it?
Comment: TPM vs FPKM divergence at high values
by
pinheirofabiano
▴ 110
I don't have a better mathematical explanation, but FPKMs are not reliable for gene expression studies, there are many discussions about t…
Comment: TPM vs FPKM divergence at high values
by
megancgrdnr
• 0
Thank you for your answer! Do you have any sense of why the expression values diverge at higher-expressed genes? I can't see anything in th…
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