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122,125 results • Page
1 of 2443
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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
Kevin Blighe
89k • written 3.5 years ago by
mohsamir2016
▴ 30
2
votes
4
replies
5.3k
views
Extract transcript fasta using gff
fasta
gff
updated 3 hours ago by
Bourumir
▴ 10 • written 4.4 years ago by
boczniak767
▴ 880
0
votes
3
replies
167
views
Batch Effect
batch
effect
updated 4 hours ago by
jared.andrews07
★ 19k • written 23 hours ago by
Umair
• 0
0
votes
1
reply
475
views
MDS file NaN values
missing
genome
MDS
updated 1 hour ago by
Kevin Blighe
89k • written 3 months ago by
am29
▴ 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
Kevin Blighe
89k • written 12 weeks ago by
Luwell
• 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
Kevin Blighe
89k • written 12 weeks ago by
bioinfo
▴ 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
Biostar
3.7k • written 8.9 years ago by
Istvan Albert
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
Kevin Blighe
89k • written 13 days ago by
a.papadam
• 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
Kevin Blighe
89k • written 15 days ago by
Vojtěch
• 0
0
votes
1
reply
442
views
useing lncHUB2 with R
Genelist
lncHUB2
Rprograming
lncRNAs
updated 1 hour ago by
Kevin Blighe
89k • written 16 days ago by
mastoreh
• 0
0
votes
1
reply
339
views
interpretation of the results obtained with digital PCR
dPCR
updated 1 hour ago by
Kevin Blighe
89k • written 22 days ago by
Lorenzo
• 0
4
votes
7
replies
240
views
A question of NGS requirement
storage
RNAseq
updated 6 hours ago by
GenoMax
154k • written 11 hours ago by
zizigolu
★ 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
GenoMax
154k • written 14 hours ago by
dheeraj
• 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
Kevin Blighe
89k • written 16 days ago by
mastoreh
• 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
Kevin Blighe
89k • written 16 days ago by
mastoreh
• 0
3
votes
3
replies
1.4k
views
install SCP problem
SCP
updated 8 hours ago by
Kevin Blighe
89k • written 2.4 years ago by
Andy
▴ 140
0
votes
2
replies
650
views
exploring scRNA with only one sample per condition
scRNAseq
exploring
updated 20 hours ago by
Kevin Blighe
89k • written 16 days ago by
Mery
• 0
0
votes
1
reply
450
views
Doubt on protein preparation before Vina
protein
docking
Vina
doubt
updated 20 hours ago by
Kevin Blighe
89k • written 12 days ago by
Ria
• 0
0
votes
7
replies
730
views
Upstream (5′) Coverage Depletion Observed in IGV
igv
ont
updated 1 hour ago by
Kevin Blighe
89k • written 11 days ago by
safeassli
▴ 10
1
vote
5
replies
1.5k
views
Weird edgeR normalization results for one tissue
edgeR
Normalization
RNAseq
updated 1 hour ago by
Kevin Blighe
89k • written 17 days ago by
imetrev
▴ 10
0
votes
1
reply
457
views
Optimal way of running sysvi / scanvi
single-cell
scanvi
integration
updated 1 hour ago by
Kevin Blighe
89k • written 10 days ago by
LChart
5.2k
0
votes
10
replies
998
views
Interpretation of logFC in limma-voom contrasts
limma
logFC
limma-voom
updated 21 hours ago by
Kevin Blighe
89k • written 9 days ago by
donan
• 0
1
vote
1
reply
385
views
Rescaling after relative abundance filtering of gut microbiome data
microbiome
gut
network
updated 1 hour ago by
Kevin Blighe
89k • written 8 days ago by
yesquokkan
• 0
1
vote
5
replies
642
views
lollipop plot showing DNA sequence
mutation
plot
lollipop
updated 1 hour ago by
Kevin Blighe
89k • written 8 days ago by
varga.luca
• 0
0
votes
1
reply
315
views
Germline and somatic mutations TCGA (GDC Data Portal)
germline
somatic
TCGA
mutation
updated 1 hour ago by
Kevin Blighe
89k • written 7 days ago by
stubbe1charlotte
• 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
Kevin Blighe
89k • written 6 days ago by
Nishant
• 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
Kevin Blighe
89k • written 5 days ago by
Pranava
▴ 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
Kevin Blighe
89k • written 5 days ago by
bobia9193
▴ 20
0
votes
1
reply
218
views
Fst and SNPs
Fst
R
snps
ddrad
updated 1 hour ago by
Kevin Blighe
89k • written 4 days ago by
md2022
• 0
0
votes
2
replies
251
views
Autosome/ sex chromosome assembly error
genomics
analysis
sexchromosome
tools
updated 21 hours ago by
Kevin Blighe
89k • written 4 days ago by
Megan
• 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
Kevin Blighe
89k • written 3 days ago by
Laura
• 0
0
votes
2
replies
260
views
Polyadenylation-PAS sites APAlyzer
R
package
bioinformatics
updated 21 hours ago by
Kevin Blighe
89k • written 3 days ago by
aj123
▴ 140
1
vote
3
replies
316
views
Mixed marker expression in Xenium data
Clustering
Xenium
explorer
updated 21 hours ago by
Kevin Blighe
89k • written 2 days ago by
Song
▴ 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
Kevin Blighe
89k • written 2 days ago by
城玮
• 0
0
votes
2
replies
216
views
Comparison of different RNAseq data sets
DEG
batch
RNAseq
effect
updated 1 hour ago by
Kevin Blighe
89k • written 1 day ago by
DrSmad
• 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
Kevin Blighe
89k • written 23 hours ago by
murheisa
• 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
colindaven
8.1k • written 20 months ago by
soyeon
• 0
1
vote
1
reply
191
views
Set parameters of fastsimcoal2.
fastsimcoal2
updated 1 day ago by
GenoMax
154k • written 1 day ago by
haoma
• 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
ATpoint
90k • written 2 days ago by
arashsltni
• 0
4
votes
15
replies
5.9k
views
8 follow
Data retrieval from GEO
Microarray
GEO
updated 2 days ago by
GenoMax
154k • written 8.2 years ago by
lessismore
★ 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
jim_grigor
• 0 • written 2.9 years ago by
Novogene
▴ 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
ATpoint
90k • written 28 days ago by
aj123
▴ 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
xinuke
▴ 70
1
vote
2
replies
321
views
deep learning architectures
Deep
learning
bioinformatics
updated 3 days ago by
LChart
5.2k • written 3 days ago by
Deepanshu
• 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
colindaven
8.1k • written 4 days ago by
scsc185
▴ 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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kingcohn
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Physalia-courses
★ 2.7k
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★ 4.4k
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154k
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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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