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121,566 results • Page
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Forum:
LogFC on geometric means vs on arithmetic means. Presto vs Seurat
Presto
Seurat
logFC
general
questions
just now by
e.r.zakiev
▴ 260
1
vote
1
reply
321
views
Question about anova-like test using Limma
makeContrasts
limma
updated 11 minutes ago by
Gordon Smyth
★ 8.2k • written 13 months ago by
Daniel
▴ 10
0
votes
0
replies
10
views
Refflat file for Rattus norvegicus
file
RefFlat
Rattus
RNA-seq
norvegicus
46 minutes ago by
AIMAR
▴ 50
0
votes
3
replies
81
views
asking for optimized bash scripting
analysis
updated just now by
ATpoint
88k • written 6 hours ago by
QX
▴ 70
0
votes
3
replies
71
views
Differential expression genes
SEQ
DGE
RNA
updated 59 minutes ago by
Arup Ghosh
3.3k • written 3 hours ago by
m90
▴ 30
0
votes
2
replies
66
views
Discrepancy Between Fragment Size Distribution and MACS3-Predicted Fragment Length in ChIP-seq Dataset
macs3
updated 2 hours ago by
ATpoint
88k • written 3 hours ago by
christoph.neu
▴ 10
843
votes
170
replies
182k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 11 weeks ago by
Biostar
3.6k • written 8.6 years ago by
Istvan Albert
102k
1
vote
2
replies
91
views
Plotting of genes using tpm matrix
normalization
TPM
boxplot
updated 3 hours ago by
i.sudbery
21k • written 6 hours ago by
rajdeepboral00
▴ 70
3
votes
2
replies
109
views
A question about model matrix and contrast
makeContrasts
limma
20 minutes ago by
jkim
▴ 210
0
votes
1
reply
265
views
Understanding MAG completeness and contig composition in metagenomic bins
data
shotgun
updated 5 hours ago by
andres.firrincieli
3.9k • written 5 days ago by
shevch2009
▴ 20
2
votes
4
replies
228
views
Understanding NCBI vs ENA data
ENA
NCBI
SRA
updated 2 hours ago by
GenoMax
152k • written 1 day ago by
wes
▴ 90
0
votes
2
replies
141
views
Job:
Assistance running population specific hapibd
ancestry
haplotype
IBD
updated 10 hours ago by
cmdcolin
★ 4.2k • written 17 hours ago by
CJ169
• 0
2
votes
1
reply
110
views
Empty result using enrichGO
clusterProfiler
updated 14 hours ago by
GenoMax
152k • written 21 hours ago by
Chris
▴ 360
2
votes
1
reply
5.7k
views
Convert ct file to dot bracket format
RNA
structure
updated 19 hours ago by
zahraniasari.2023
• 0 • written 8.6 years ago by
abdullahrenk
▴ 30
0
votes
2
replies
907
views
News:
Hands-On Workshop - Next-Generation Sequencing Data Analysis: A Practical Introduction (September 10-12, 2025 in Berlin, Germany)
Workshop
RNA-Seq
Illumina
VariantCalling
DNA-Seq
21 hours ago by
ecSeq Bioinformatics
▴ 20
0
votes
0
replies
66
views
Is it possible to perform XP-EHH and iHS on targeted sequencing data without a .map file?
ngs
ihs
analysis
selection
sequencing
1 day ago by
slzr_
▴ 10
0
votes
0
replies
74
views
Discrepancy in RNA editing calls between STAR and Subjunc aligners using JACUSA2
jacusa2
rnaseq
subjunc
star
rsubread
1 day ago by
thomas.heigl.ibk
• 0
2
votes
1
reply
123
views
RNA-Seq paired-end datasets
paired-end
RNA-seq
Bioinformatic
updated 1 day ago by
Matthias Zepper
5.1k • written 1 day ago by
AIMAR
▴ 50
0
votes
0
replies
114
views
News:
Course: Introduction to CRISPR
GenomeEditing
CRISPR
Evolution
1 day ago by
Physalia-courses
★ 2.6k
2
votes
3
replies
329
views
Best strategy for comparing cell-type composition between disease and healthy groups in single-cell RNA-seq data
Single_cell
updated 1 hour ago by
ATpoint
88k • written 1 day ago by
城玮
• 0
1
vote
4
replies
262
views
RNA-seq assigned alignments
paired-end
STAR
RNA-seq
mapping
single-end
updated 1 day ago by
jaro.slamecka
▴ 270 • written 2 days ago by
Manko47
▴ 10
0
votes
1
reply
187
views
Obtain Common SNPS for Mouse Genome
mouse
SNPs
updated 2 days ago by
GenoMax
152k • written 2 days ago by
joe_genome
▴ 60
1
vote
3
replies
351
views
How do you clean GEO metadata before downstream analysis?
geo
updated 1 day ago by
yura.grabovska
▴ 800 • written 3 days ago by
Alba
• 0
0
votes
1
reply
187
views
Seeking high-quality curated metabolic models with time-resolved flux data for sonification project
metabolism
sonification
networks
updated 2 days ago by
Mensur Dlakic
★ 29k • written 2 days ago by
omereilam1
• 0
0
votes
0
replies
135
views
Standard way to represent represent indel (insertion or deletion) alleles within a haplotype
haplotypes
indels
haploview
2 days ago by
Mwangana
• 0
1
vote
1
reply
256
views
lovis4u Configuration
graph
lovis4u
genomics
updated 3 days ago by
GenoMax
152k • written 3 days ago by
NIkita
• 0
1
vote
1
reply
282
views
Tool:
Tool to clean GEO metadata
GEO
metadata
updated 2 days ago by
yura.grabovska
▴ 800 • written 3 days ago by
Alba
• 0
1
vote
2
replies
537
views
WGBS Analysis with 1 control sample and 6 disease samples
one
WGBS
sample
updated 3 days ago by
ATpoint
88k • written 14 days ago by
Cassandra
▴ 10
0
votes
2
replies
549
views
How to extract gene list from GEO dataset in R
coding
beginner
question
r
updated 4 days ago by
Shohel
• 0 • written 14 days ago by
decorus
• 0
0
votes
6
replies
517
views
RNA seq strandedness (reverse-strand)
seq
reverse-stranded
strand
RNA
2 days ago by
ZuelTech
• 0
0
votes
0
replies
203
views
TFs and enrichment analysis for TRAP sequencing
TRAP
4 days ago by
Genesis
• 0
0
votes
2
replies
311
views
Extract track data from "search by region" feature on ENCODE
Encode
2 days ago by
AlienPumpkinPie
• 0
9
votes
8
replies
987
views
Weird p-value distribution on edgeR results
edgeR
pvalue-distribution
gene-expression
updated 4 days ago by
dariober
15k • written 13 days ago by
Guillermo
▴ 30
1
vote
3
replies
346
views
Draw GO tree for some GO ids with coloring
enrichment
GO
4 days ago by
boczniak767
▴ 880
2
votes
4
replies
2.7k
views
Extract transcript fasta using gff
fasta
gff
updated 4 days ago by
cmdcolin
★ 4.2k • written 4.1 years ago by
boczniak767
▴ 880
1
vote
4
replies
1.2k
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 5 days ago by
Jasim
• 0 • written 15 months ago by
otieno43
▴ 40
0
votes
1
reply
282
views
calculating coverage of gene in my metagenomes with samtools
samtools
depth
metagenome
coverage
updated 5 days ago by
Pierre Lindenbaum
166k • written 5 days ago by
lintonf
• 0
2
votes
1
reply
286
views
how to merge gbz files
vg
updated 5 days ago by
Jouni Sirén
▴ 690 • written 5 days ago by
lushjia
• 0
2
votes
1
reply
276
views
plotting read length distribution of Single End data
read_length_distribution
single_end_sequencing
WGS
5 days ago by
Meghan.T
▴ 10
4
votes
1
reply
329
views
Preranked GSEA permutation
GSEA
updated 5 days ago by
ATpoint
88k • written 6 days ago by
as823jk
• 0
2
votes
2
replies
422
views
why bwa-mem only return one read with pair-read end
sequencing
bwa-mem
updated 3 days ago by
rfran010
★ 1.6k • written 6 days ago by
QX
▴ 70
0
votes
2
replies
306
views
Identification problem of IDE-8 cell on culture with inverted microscope
IDE-8
offtopic
updated 1 day ago by
i.sudbery
21k • written 5 days ago by
Prashanta
• 0
0
votes
2
replies
392
views
Identifying RBP motifs overlapping exons
motifs
bedtools
RBP
updated 5 days ago by
GenoMax
152k • written 9 days ago by
RK
• 0
0
votes
0
replies
238
views
News:
Upcoming NGS Data Analysis Courses 2025
SingleCell
RNAseq
Epigenomics
Illumina
DNAseq
5 days ago by
ecSeq Bioinformatics
▴ 20
0
votes
1
reply
304
views
How to match clinical information with expression data in R
R
updated 6 days ago by
Arup Ghosh
3.3k • written 6 days ago by
py3296746920
• 0
3
votes
1
reply
475
views
Identify SNP, Indel variants from a List of FASTA sequence
SNP
updated 6 days ago by
Mark
★ 1.7k • written 11 days ago by
Trinh
▴ 10
2
votes
15
replies
990
views
Which Reference Hg38 or T2T?? Both??
Host
Removal
6 days ago by
Jon
• 0
3
votes
2
replies
373
views
Can I transduce HEK293T with Cas9 lentivirus followed by transfection with sgRNAs?
lentivirus
Transduction
CRISPR
transfection
offtopic
updated 6 days ago by
jared.andrews07
★ 19k • written 6 days ago by
louisflower1999
• 0
3
votes
3
replies
441
views
Mitochondrial annotation tool for algae
barcoding
annotation
updated 7 days ago by
Juke34
9.3k • written 7 days ago by
firefox91
• 0
1
vote
2
replies
399
views
Identifying gene outliers in a genome using composition analysis.
RSCU
composition
GC
outliers
updated 7 days ago by
GenoMax
152k • written 7 days ago by
Shakunthala Natarajan
• 0
121,566 results • Page
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Answer: Question about anova-like test using Limma
Answer: A question about model matrix and contrast
Comment: Plotting of genes using tpm matrix
A question about model matrix and contrast
Answer: A question about model matrix and contrast
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Answer: Best strategy for comparing cell-type composition between disease and healthy gr
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Comment: asking for optimized bash scripting
by
ATpoint
88k
It's fine. You can add some spacing for better readability, but tbh, it exactly serves your purpose, is simple (therefore nothing fancy can…
Answer: Question about anova-like test using Limma
by
Gordon Smyth
★ 8.2k
> am I testing the group effect while controlling for the variables TechA, TechB, and TechC? Yes, that is correct.
Comment: A question about model matrix and contrast
by
jkim
▴ 210
Thanks a lot, Dr. Smyth!
Answer: asking for optimized bash scripting
by
cmdcolin
★ 4.2k
the script you wrote is fairly small so there's not that much I would do to change it, but AI coding helpers are pretty good writing a lot …
Comment: Differential expression genes
by
Arup Ghosh
3.3k
Try [trinityrnaseq][1]. [1]: http://github.com/trinityrnaseq/trinityrnaseq
Comment: Differential expression genes
by
m90
▴ 30
So kallisto will do DE on transcript level ?or gene level? Because I need on gene level and another question using RNA seq or mRNA seq wil…
Comment: Best strategy for comparing cell-type composition between disease and healthy gr
by
ATpoint
88k
Agreed. The lack of either biological replication at all (no hashed samples by donor etc or one lane per donor), the lack of using existing…
Comment: Differential expression genes
by
GenoMax
152k
Depends on whether you are working with a prokaryote or a Eukaryote. You could use `FINDER` ([**LINK**][1]) for eukaryotes. When you assemb…
Comment: Discrepancy Between Fragment Size Distribution and MACS3-Predicted Fragment Leng
by
ATpoint
88k
Two things: A) I would check the library in the Bioanalyzer rather than the chromatin, since the library prep might bias the distribution a…
Comment: Discrepancy Between Fragment Size Distribution and MACS3-Predicted Fragment Leng
by
GenoMax
152k
> Should the fragment size determined by the Bioanalyzer (Agilent assay) and the fragment length predicted by MACS3 be the same, or at leas…
Comment: Understanding NCBI vs ENA data
by
GenoMax
152k
While the file name seems to indicate the data is filtered, you can use `lima` ([LINK][1]) to confirm that. You will need to know which lib…
Comment: DGE analysis in Seurat using paired samples per donor ?
by
Picasa
▴ 690
I have already defined sub population, the idea was just to do a T vs NT in each cluster (without doing pseudobulk)
Answer: asking for optimized bash scripting
by
Joe
22k
You can set global ("environment" variables) in bash, but they aren't generally the right way to do this. The "right" way to do this in my…
Comment: Plotting of genes using tpm matrix
by
i.sudbery
21k
To add to what @ATPoint was saying: TPM is fine for comparing the expression of two genes within a single condition (or at least, is proba…
Comment: Plotting of genes using tpm matrix
by
ATpoint
88k
Scaling is only necessary if you have genes with different expression levels, so you probably can go ahead. For differential expression of …
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