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122,125 results • Page 1 of 2443
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11
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Forum: vg dist on (large) graph runtime?
vg
1 hour ago by kingcohn ▴ 30
0
votes
2
replies
722
views
Confusion regarding Euclidean distance measures of dissimilarity
RNAseq R EdgeR
updated 1 hour ago by 89k • written 3.5 years ago by ▴ 30
2
votes
4
replies
5.3k
views
Extract transcript fasta using gff
fasta gff
updated 3 hours ago by ▴ 10 • written 4.4 years ago by ▴ 880
0
votes
3
replies
167
views
Batch Effect
batch effect
updated 4 hours ago by ★ 19k • written 23 hours ago by • 0
0
votes
1
reply
475
views
MDS file NaN values
missing genome MDS
updated 1 hour ago by 89k • written 3 months ago by ▴ 60
0
votes
1
reply
706
views
How to decide the normalization method for targeted metabolomics data ?
LC-MS normalization R metabolomics targeted-metabolomics
updated 7 hours ago by 89k • written 12 weeks ago by • 0
0
votes
1
reply
2.7k
views
Best Practice for Group Composition Plots in Phyloseq
phyloseq microbiome relative-abundance
updated 7 hours ago by 89k • written 12 weeks ago by ▴ 60
850
votes
173
replies
218k
views
113 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook training
updated 17 days ago by 3.7k • written 8.9 years ago by 103k
0
votes
3
replies
670
views
Sea of genomic wide significant hits in GWAS (Plink2) and Absence when using regenie
Genome-wide GWAS snps regenie plink2
updated 7 hours ago by 89k • written 13 days ago by • 0
0
votes
4
replies
1.5k
views
Can a spiked-in negative control still be considered a true negative control in 16S sequencing?
sequencing
updated 1 hour ago by 89k • written 15 days ago by • 0
0
votes
1
reply
442
views
useing lncHUB2 with R
Genelist lncHUB2 Rprograming lncRNAs
updated 1 hour ago by 89k • written 16 days ago by • 0
0
votes
1
reply
339
views
interpretation of the results obtained with digital PCR
dPCR
updated 1 hour ago by 89k • written 22 days ago by • 0
4
votes
7
replies
240
views
A question of NGS requirement
storage RNAseq
updated 6 hours ago by 154k • written 11 hours ago by ★ 4.4k
0
votes
0
replies
59
views
Feature selection for multi-class classification problem.
feature M3Drop R Python selection
10 hours ago by Shakunthala Natarajan • 0
1
vote
1
reply
109
views
Forum: How can I start learning bioinformatics? Any recommended beginner-friendly resources?
learning-resources beginners bioinformatics
updated 14 hours ago by 154k • written 14 hours ago by • 0
0
votes
1
reply
460
views
R code for getting TFs from ChEA2024 by gene list
TF ChEA2024 Rprograming Genelist
updated 1 hour ago by 89k • written 16 days ago by • 0
0
votes
2
replies
553
views
R code for getting miRNAs from miRTarBase and TargetScan by gene list
miRTarBase Genelist Rcode TargetScan
updated 8 hours ago by 89k • written 16 days ago by • 0
3
votes
3
replies
1.4k
views
install SCP problem
SCP
updated 8 hours ago by 89k • written 2.4 years ago by ▴ 140
0
votes
2
replies
650
views
exploring scRNA with only one sample per condition
scRNAseq exploring
updated 20 hours ago by 89k • written 16 days ago by • 0
0
votes
1
reply
450
views
Doubt on protein preparation before Vina
protein docking Vina doubt
updated 20 hours ago by 89k • written 12 days ago by • 0
0
votes
7
replies
730
views
Upstream (5′) Coverage Depletion Observed in IGV
igv ont
updated 1 hour ago by 89k • written 11 days ago by ▴ 10
1
vote
5
replies
1.5k
views
Weird edgeR normalization results for one tissue
edgeR Normalization RNAseq
updated 1 hour ago by 89k • written 17 days ago by ▴ 10
0
votes
1
reply
457
views
Optimal way of running sysvi / scanvi
single-cell scanvi integration
updated 1 hour ago by 89k • written 10 days ago by 5.2k
0
votes
10
replies
998
views
Interpretation of logFC in limma-voom contrasts
limma logFC limma-voom
updated 21 hours ago by 89k • written 9 days ago by • 0
1
vote
1
reply
385
views
Rescaling after relative abundance filtering of gut microbiome data
microbiome gut network
updated 1 hour ago by 89k • written 8 days ago by • 0
1
vote
5
replies
642
views
lollipop plot showing DNA sequence
mutation plot lollipop
updated 1 hour ago by 89k • written 8 days ago by • 0
0
votes
1
reply
315
views
Germline and somatic mutations TCGA (GDC Data Portal)
germline somatic TCGA mutation
updated 1 hour ago by 89k • written 7 days ago by • 0
1
vote
5
replies
488
views
Obtaining DESeq2 LFC values for Loadings of Principal Components
RNAseq Model DESeq2 Design PCA
updated 1 hour ago by 89k • written 6 days ago by • 0
0
votes
1
reply
255
views
Exploring cross-cancer similarity using SNP or variant data with deep learning
tcga deep-learning snp cancer
updated 1 hour ago by 89k • written 5 days ago by ▴ 30
0
votes
3
replies
394
views
Batch correction with ComBat for samples from multiple sampling sites
batch-correction ComBat
updated 1 hour ago by 89k • written 5 days ago by ▴ 20
0
votes
1
reply
218
views
Fst and SNPs
Fst R snps ddrad
updated 1 hour ago by 89k • written 4 days ago by • 0
0
votes
2
replies
251
views
Autosome/ sex chromosome assembly error
genomics analysis sexchromosome tools
updated 21 hours ago by 89k • written 4 days ago by • 0
0
votes
1
reply
295
views
How should I interpret GSEA results for the C6: Oncogenic Signatures collection (e.g., MYC_UP.V1_DN)?
RNA-seq Oncogenic MSigDB GSEA pathways
updated 1 hour ago by 89k • written 3 days ago by • 0
0
votes
2
replies
260
views
Polyadenylation-PAS sites APAlyzer
R package bioinformatics
updated 21 hours ago by 89k • written 3 days ago by ▴ 140
1
vote
3
replies
316
views
Mixed marker expression in Xenium data
Clustering Xenium explorer
updated 21 hours ago by 89k • written 2 days ago by ▴ 10
3
votes
3
replies
341
views
Help interpreting antiSMASH BGCs for EPA (eicosapentaenoic acid) biosynthesis
biosynthetic_gene_cluster secondary_metabolism PKS heterologous_expression
updated 21 hours ago by 89k • written 2 days ago by • 0
0
votes
2
replies
216
views
Comparison of different RNAseq data sets
DEG batch RNAseq effect
updated 1 hour ago by 89k • written 1 day ago by • 0
0
votes
1
reply
99
views
reference genome into chromosomes but annotation only at scaffolds level
reference rnaseq genome scaffolds annotation
updated 22 hours ago by 89k • written 23 hours ago by • 0
0
votes
0
replies
121
views
News: Course: Multimodal AI for Systems Biology (Online, 2–6 March 2026)
Genomics multimodalAI MultiOmics
1 day ago by Physalia-courses ★ 2.7k
4
votes
4
replies
850
views
cufflinks- cuffquant issue
cufflinks
updated 1 day ago by 8.1k • written 20 months ago by • 0
1
vote
1
reply
191
views
Set parameters of fastsimcoal2.
fastsimcoal2
updated 1 day ago by 154k • written 1 day ago by • 0
2
votes
1
reply
240
views
Is it possible to reverse a VST transformation to obtain original counts?
bulkRNAseq VST-transformed_matrix
updated 2 days ago by 90k • written 2 days ago by • 0
4
votes
15
replies
5.9k
views
8 follow
Data retrieval from GEO
Microarray GEO
updated 2 days ago by 154k • written 8.2 years ago by ★ 1.4k
8
votes
2
replies
20k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
updated 2 days ago by • 0 • written 2.9 years ago by ▴ 510
0
votes
2
replies
765
views
News: Only 8 places left - 1st Berlin Winter School in RNA-Seq Data Analysis (Dec 8-11, 2025)
Transcriptomics RNA-Seq Expression Differential
2 days ago by ecSeq Bioinformatics ▴ 20
0
votes
0
replies
177
views
News: Workshop: Virtual Genome Annotation, November 18–20
GenomeAnnotation workshop UConn
2 days ago by zsc25001 ▴ 10
5
votes
5
replies
932
views
hisat2 error-Paired end reads not equal or lack of RAM/disk space?
end fastq paired
updated 21 days ago by 90k • written 28 days ago by ▴ 140
47
votes
17
replies
17k
views
11 follow
Forum: Is Software Development a key part of Bioinformatics?
Software-Development
written 10.8 years ago by ▴ 70
1
vote
2
replies
321
views
deep learning architectures
Deep learning bioinformatics
updated 3 days ago by 5.2k • written 3 days ago by • 0
2
votes
1
reply
322
views
Creating a personalized genome assembly for read simulation from illumina WGS data
illumina consensus wgs phasing simulation
updated 3 days ago by 8.1k • written 4 days ago by ▴ 80
122,125 results • Page 1 of 2443
Recent Votes
A: Counting mismatched characters from sequences from a fasta file in comparison to
Comment: A question of NGS requirement
C: Count how many gaps and mismatches using pairwise2 alignment
Answer: How to extract protein sequences from a .gff file
Answer: A question of NGS storage requirement
Comment: A question of NGS storage requirement
A: converting RefSeq Protein (NCBI) accession numbers to Gene Symbol
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Popular Question to kingcohn ▴ 30
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Recent Replies
Answer: Confusion regarding Euclidean distance measures of dissimilarity by Kevin Blighe 89k
Finally answered 3.5 years later now that I have time.... Hey, I appreciate you reaching out directly - happy to try to help with thi…
Comment: Driver Phylogenetic Trees of TRACERx project by Kevin Blighe 89k
Note: a few years later, Achilles Therapeutics went into liquidation.
Comment: Batch Effect by jared.andrews07 ★ 19k
I would not consider the flow cell meaningfully and clearly impacting things based on your non-batch corrected plots. I'd leave it out of y…
Comment: Batch Effect by Umair • 0
Thank you Kevin for your reply. Kindly, can you advise me after checking the PCAs of my dataset? ![enter image description here][1] ![ente…
Comment: A question of NGS requirement by GenoMax 154k
One can never have enough storage but that said the PromethION cells were more in the ~ 1.5 TB size in my experience. So the amount you men…
Answer: MDS file NaN values by Kevin Blighe 89k
Hello am29, I've seen this kind of issue crop up a few times when merging datasets for population structure analyses, especially with refe…
Answer: How to decide the normalization method for targeted metabolomics data ? by Kevin Blighe 89k
Hey, Thanks for providing the details of your setup and the screenshots - it helps a lot to understand what's going on. I'll try to addr…
Answer: Best Practice for Group Composition Plots in Phyloseq by Kevin Blighe 89k
Method B is indeed the standard and recommended approach in phyloseq for group-level composition plots, as seen in official examples and tu…
Answer: Sea of genomic wide significant hits in GWAS (Plink2) and Absence when using reg by Kevin Blighe 89k
Hey, Thanks for posting - always good to see GWAS discussions here. I'll try to address your query based on what you've shared (includin…
Answer: Can a spiked-in negative control still be considered a true negative control in by Kevin Blighe 89k
Hey there, You're raising a valid point here, and it's a common debate in microbiome workflows, especially with low-biomass samples or whe…
Answer: useing lncHUB2 with R by Kevin Blighe 89k
Hi, I see you're trying to batch query for related lncRNAs from a gene list using the lncHUB2 site, but it only supports single queries vi…
Answer: interpretation of the results obtained with digital PCR by Kevin Blighe 89k
Hello, Thanks for the details on your setup. I'll keep this concise, focusing on standard dPCR practices (e.g., per dMIQE guidelines). ##…
Comment: A question of NGS storage requirement by zizigolu ★ 4.4k
so If we also keep the raw signal files (FAST5/POD5) for possible re-basecalling later, the 60–70 TB over the full project makes sense or …
Comment: A question of NGS storage requirement by GenoMax 154k
What kind of sequencing are you thinking of doing? Direct RNA or normal cDNA? Assuming cDNA you may only need 10 cells (with barcoding an…
Comment: A question of NGS requirement by zizigolu ★ 4.4k
Thanks all
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