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122,072 results • Page
2 of 2442
Sort: Rank
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Votes
Replies
0
votes
0
replies
307
views
Error "no rows to aggregate" using makeFunctionalPrediction() Tax4fun2
R
Tax4fun2
prediction
functional
makeFunctionalPrediction
9 days ago by
Marine
• 0
7
votes
8
replies
2.6k
views
Is there a way to produce/convert nhmmer output to a bed file?
bed
nhmmer
updated 10 days ago by
colindaven
8.0k • written 5.0 years ago by
jamie.pike
▴ 90
0
votes
3
replies
518
views
Python deconvolution tools for bulk RNA-seq data
RNA-seq
bulk-rna-seq
Deconvolution
python
transcriptomics
23 hours ago by
AlexStar
▴ 200
1
vote
1
reply
341
views
Unique insertion sites Calculation from Himar1 C9 based TnSeq
Kossivi
updated 10 days ago by
GenoMax
154k • written 10 days ago by
Kossivi
• 0
2
votes
5
replies
507
views
BWA-MEM with an array of files
alignment
array
BWA-MEM
updated 10 days ago by
LChart
5.1k • written 10 days ago by
garcesj
▴ 50
0
votes
0
replies
268
views
interpretation of the results obtained with digital PCR
dPCR
10 days ago by
Lorenzo
• 0
0
votes
0
replies
340
views
Job:
Sr. Manager, Clinical Data Science at InterVenn Biosciences
statistics
glycoproteomics
proteomics
machine-learning
omics
10 days ago by
Daniel
• 0
2
votes
1
reply
387
views
Modeling/simulations using SNPs data
SNP
updated 11 days ago by
Dave Carlson
★ 2.2k • written 11 days ago by
Gonzalo
• 0
2
votes
1
reply
376
views
Strugling on the 3'rule of HGVS
notation
hgvs
variants
updated 11 days ago by
Jeremy Leipzig
23k • written 11 days ago by
lacb
▴ 120
13
votes
17
replies
5.1k
views
Extract fastq sequences based on date/time (which is in the header)
sequence
fastq
updated 11 days ago by
zhanxw
▴ 20 • written 7.1 years ago by
a.b.g
▴ 10
2
votes
5
replies
3.2k
views
Filter nanopore fastq files by start time
nanopore
fastq
filter
start time
updated 11 days ago by
zhanxw
▴ 20 • written 6.3 years ago by
sendhelp
▴ 10
3
votes
4
replies
482
views
Discrepancy in Q-score assessment of ONT reads in Nanopore and third-party software repors
seqkit
q-score
fastqc
16s-wf
nanoplot
11 days ago by
k-tarasov
▴ 10
4
votes
4
replies
765
views
How to create a consensus of a contig with samtools or bbmap?
contig
bbmap
consensus
samtools
genome
updated 11 days ago by
jkbonfield
★ 1.3k • written 22 days ago by
marongiu.luigi
▴ 770
2
votes
3
replies
509
views
Validating snRNA-seq cell type by correlating with other datasets
RNA-seq
scRNA-seq
snRNA-seq
updated 8 days ago by
ATpoint
89k • written 12 days ago by
Ben
• 0
0
votes
1
reply
325
views
Configuration file for DSP WTA
DSP
updated 11 days ago by
GenoMax
154k • written 12 days ago by
Petesview
▴ 10
0
votes
0
replies
265
views
News:
1st Berlin Winter School in RNA-Seq Data Analysis (Dec 8-11, 2025)
Transcriptomics
RNA-Seq
Expression
Differential
12 days ago by
ecSeq Bioinformatics
▴ 20
0
votes
2
replies
458
views
What is the length of the longest ORF appearing in reading frame 2 of any of the sequences?
python
12 days ago by
fra.r.silvestro
▴ 10
0
votes
1
reply
368
views
Does the weights file stay the same for a different model organism
machine-learning
updated 5 days ago by
Ram
45k • written 12 days ago by
Sharma
• 0
0
votes
2
replies
446
views
HDOCK Server Error!
HDOCK
Docking
10 days ago by
Jannatul Ferdous
• 0
3
votes
1
reply
361
views
Variant Normalization
vcf
updated 12 days ago by
Istvan Albert
103k • written 12 days ago by
spesks
• 0
1
vote
2
replies
875
views
Should differential expression analysis be incorporated in cross validation for training machine learning models?
RNA-seq
DEA
TCGA
Learning
Machine
12 days ago by
yordany.perdigon
• 0
0
votes
0
replies
292
views
News:
Autumn School in Bioinformatics – Online, 20–24 October
NGS
Phylogenomics
RNAseq
Singularity
Docker
updated 12 days ago by
Pierre Lindenbaum
166k • written 12 days ago by
Physalia-courses
★ 2.7k
0
votes
1
reply
341
views
Issue with Snippy 4.6.0
Snippy
Core.vcf
SNP
updated 12 days ago by
GenoMax
154k • written 12 days ago by
bioinfo_enthusiast
• 0
0
votes
2
replies
442
views
Cells from normal sample were incorrectly classified as tumor cells using copykat
copykat
scRNA-seq
cell
tumor
11 days ago by
tujuchuanli
▴ 140
0
votes
1
reply
345
views
NOVOPlasty assembly fails with “INVALID SEED” using first read as seed
mitochondria
Assembly
Genome
Novoplasty
updated 12 days ago by
GenoMax
154k • written 13 days ago by
Buddha
• 0
3
votes
1
reply
409
views
1 vs 1 DEG analysis in scrna seq data
DEG
updated 13 days ago by
ATpoint
89k • written 14 days ago by
carolofharvest
▴ 50
22
votes
13
replies
1.5k
views
6 follow
GUI commercial software for 10x single cell gene expression analysis
single-cell
software
commercial
gui
13 days ago by
firestar
★ 1.7k
1
vote
0
replies
331
views
Tool:
ORFanage: by-reference protein annotation and comparison for transcriptome assembly
orf
rna-seq
assembly
annotation
transcriptome
14 days ago by
Ales
▴ 90
0
votes
2
replies
623
views
scVI vs Harmony, which is better for cell type based clustering in brain tissue?
harmony
scVI
single
cell
updated 15 days ago by
ATpoint
89k • written 19 days ago by
biotrekker
▴ 110
1
vote
0
replies
345
views
News:
Manual Genome Curation using PretextView course
Genome-Assembly
PretextView
HI-C
Manuel-Curation
16 days ago by
Physalia-courses
★ 2.7k
7
votes
14
replies
1.3k
views
DESeq2 on metagenome KO counts
abundance
KEGG
KO
deseq
metagenome
gene
updated 3 days ago by
andres.firrincieli
3.9k • written 17 days ago by
young_bioinformatician
▴ 250
0
votes
0
replies
365
views
News:
Introduction to Processing and Analysis of Spatial Multiplexed Proteomics Data
Spatial
Proteomics
omics
updated 16 days ago by
GenoMax
154k • written 16 days ago by
oliverhooker
▴ 110
2
votes
1
reply
432
views
FACS quality control based on size and doublet detection in scRNA-seq
single-cell
rna-detection
FACS
doublet
scRNA-seq
updated 13 days ago by
Ram
45k • written 16 days ago by
carolofharvest
▴ 50
1
vote
1
reply
499
views
combine VCF from diploid reference/haplotypes for the same sample
bcftools
combine
VCF
updated 15 days ago by
cmdcolin
★ 4.3k • written 16 days ago by
Matteo Ungaro
▴ 130
4
votes
4
replies
580
views
How to handle TrEMBL proteins without gene annotation in plasma proteomics?
biomarker
uniprot
proteomics
annotation
trembl
updated 16 days ago by
Elisabeth Gasteiger
★ 2.4k • written 17 days ago by
Luwell
• 0
7
votes
2
replies
488
views
Recommendations for 200 SNP markers genotyping
sequencing
DNA
genotyping
marker
updated 16 days ago by
Aleksandra
▴ 190 • written 17 days ago by
PolenP
▴ 10
0
votes
3
replies
598
views
Interpreting genomic features distribution for CUT&RUN peaks
cut_and_run
genomic
features
updated 15 days ago by
rfran010
★ 1.7k • written 18 days ago by
Rozita
▴ 40
0
votes
4
replies
670
views
hisat2 error-Paired end reads not equal or lack of RAM/disk space?
end
fastq
paired
updated 10 days ago by
ATpoint
89k • written 17 days ago by
aj123
▴ 130
1
vote
2
replies
491
views
Reasonable number of SNPs in a bacterial genome.
SNP
bacteria
updated 14 days ago by
michael.ante
★ 4.0k • written 17 days ago by
yesquokkan
• 0
2
votes
6
replies
969
views
Difficulty running FoldX in linux
DDG
foldx
updated 17 days ago by
strayeroliver
• 0 • written 19 days ago by
strayeroliver
▴ 10
0
votes
2
replies
478
views
Active site using castpfold
activesite
castpfold
Docking
updated 17 days ago by
Mensur Dlakic
★ 30k • written 17 days ago by
Ria
• 0
5
votes
12
replies
1.5k
views
6 follow
Differences between published differential gene expression results and own analysis on RNA-seq data
R
TCGA
LIMMA
updated 17 days ago by
Zhenyu Zhang
★ 1.3k • written 24 days ago by
vernonlim98
• 0
1
vote
4
replies
623
views
Problems with PacBio's Improved Phased Assembler (IPA)
pacbio
hifi
assembly
genome
17 days ago by
Panos
★ 1.8k
0
votes
6
replies
690
views
downloading raw bam files from pacbio sequencer
raw
bam_file
raw_subreads
reads
updated 17 days ago by
GenoMax
154k • written 18 days ago by
pranavdatar01
• 0
0
votes
0
replies
307
views
Best way to map biological pathways to cancer hallmarks using PLMs (without building models)?
PLM
mapping
LLM
extraction
Relation
17 days ago by
DEPANSHI
• 0
1
vote
2
replies
665
views
installation of package ‘DESeq2’ had non-zero exit status
DESeq2
updated 5 days ago by
Ram
45k • written 17 days ago by
Sarita
• 0
0
votes
1
reply
358
views
Checkm results differ from database info
Checkm
updated 13 days ago by
Ram
45k • written 17 days ago by
alevbozan18
• 0
0
votes
2
replies
1.2k
views
Transverse data
EXCEL
Unix
updated 18 days ago by
basu
• 0 • written 2.8 years ago by
Sidra
• 0
0
votes
0
replies
302
views
Is this the correct order of steps in GATK germline cohort variant calling (VQSR workflow)?
gVCF
VCF
GATK
VQSR
18 days ago by
Ramnaresh
• 0
0
votes
0
replies
315
views
How to select background metabolite sets for differential metabolite enrichment analysis?
enrichment
ORA
18 days ago by
Edward
• 0
122,072 results • Page
2 of 2442
Recent Votes
gnomAD4.0 Hail Table Downloading
Recursive reasoning for variant pathogenicity: early results show promise, need domain expertise to push further
Recursive reasoning for variant pathogenicity: early results show promise, need domain expertise to push further
Comment: reference-guided assembly tools for short read data?
Answer: Constructing a bread wheat pangenome graph using PGGB: per-chromosome vs. whole-
Setting up Aspera Connect (ascp) on Linux and macOS
Setting up Aspera Connect (ascp) on Linux and macOS
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Edward
• 0
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Physalia-courses
★ 2.7k
Popular Question
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AlexStar
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curious
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Jeremy Leipzig
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lieven.sterck
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Recent Replies
Comment: Python deconvolution tools for bulk RNA-seq data
by
AlexStar
▴ 200
I see, yes that makes sense. Could you recommend any reliable and accurate package I could use ? @atpoint MuSiC 2.0 might be a good choic…
Comment: Diffbind or DESEQ2 Chipseq data
by
james.hawley
▴ 90
The [broadPeak file format](https://macs3-project.github.io/MACS/docs/broadPeak.html) is basically a BED file with 9 columns. You can fill …
Answer: Clustering with other data type than scRNA-seq using Seurat
by
Mensur Dlakic
★ 30k
As you were told, any dimensionality reduction method could (and probably should) be used here outside of the Seurat package. In my experi…
Answer: Constructing a bread wheat pangenome graph using PGGB: per-chromosome vs. whole-
by
samuel.a.odonnell
▴ 620
> I am concerned that some known translocations in wheat might not be > captured if the graph is built separately for each chromosome. You…
Answer: Is it reasonable to keep only protein-coding genes in highly variable features i
by
ATpoint
89k
Why would you exclude them? It's genuine biological signal. Just because we/you don't know what these genes are doing doesn't mean that the…
Comment: Clustering with other data type than scRNA-seq using Seurat
by
ATpoint
89k
Sure, Bioc is generic. See for example as a guide here https://bioconductor.org/books/3.21/OSCA.basic/clustering.html#implementation In th…
Comment: Can a spiked-in negative control still be considered a true negative control in
by
GenoMax
154k
Others with more experimental experience can chime in, but if the negative controls are producing high number of non-specific reads then th…
Answer: Brave: Bioinformatics Reactive Analysis and Visualization Engine
by
Edward
• 0
I recently updated some of the code and I would like to reintroduce this GitHub open source project: BRAVE is a visual bioinformatics work…
Comment: Clustering with other data type than scRNA-seq using Seurat
by
npont
▴ 20
Thank you @atpoint and @jaredandrews07 for your help :) My data is really just a sparse matrix with genes as rows and cells as columns. …
Comment: Can a spiked-in negative control still be considered a true negative control in
by
Vojtěch
• 0
Yes, extremely high (not always, but sometimes). I think its because of PCR producing non-specific products in low mass conditions (https:/…
Comment: Some doubts about GWAS data and MR
by
Corentin
▴ 660
Just a quick comment here: the FinnGen database is mostly built from finnish participants. Due to a founder effect, Finland is quite apart …
Comment: Clustering with other data type than scRNA-seq using Seurat
by
ATpoint
89k
I would skip Seurat entirely here (and generally), and rather use more transparent methods, such as the ones in the Bioconductor framework.…
Comment: Making more complex design in limma removes significant genes
by
marek.gierlinski
▴ 50
Thank you for this clarification. Your clear explanations and generous help are greatly appreciated by everyone here.
Answer: Some doubts about GWAS data and MR
by
LChart
5.1k
It would be helpful to understand what question you're trying to answer. "Association between two diseases" could mean any or none of the f…
Comment: Redundant Genes in scRNA-seq Subclusters
by
LChart
5.1k
Unless you have replicate runs for the same sample, you won't be able to pseudobulk (since you'll be comparing k=1 to k=(N-1)). If you do h…
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