Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : today
all time
today
this week
this month
this year
35 results • Page
1 of 1
Sort: replies
Rank
Views
Votes
Replies
6
votes
10
replies
1.6k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 13 hours ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 13 hours ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
0
votes
5
replies
416
views
Removing duplicates
duplicates
ONT
minimap2
updated 5 hours ago by
joe
▴ 490 • written 20 hours ago by
quentinperriere
• 0
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 13 hours ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
0
votes
4
replies
1.7k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq
batch-effect
R
updated 13 hours ago by
Ram
43k • written 4.8 years ago by
jperezboza
▴ 20
0
votes
4
replies
263
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
52 minutes ago by
feather-W
• 0
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 13 hours ago by
Ram
43k • written 4.8 years ago by
saksis.rihards
▴ 10
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq
batch-effect
Random-Forest
updated 13 hours ago by
Ram
43k • written 4.7 years ago by
Vlad
▴ 10
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat
CNA
Batch-Effect
updated 13 hours ago by
Ram
43k • written 5.4 years ago by
sugus
▴ 150
0
votes
2
replies
177
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
20 hours ago by
mropri
▴ 150
0
votes
2
replies
198
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
19 hours ago by
DKA
▴ 40
0
votes
2
replies
219
views
How can I solve this error?
metal
4 hours ago by
22211020193
• 0
1
vote
2
replies
180
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 13 hours ago by
Ram
43k • written 15 hours ago by
aniigodwinn
• 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 13 hours ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
0
votes
2
replies
152
views
Bedmethyl file format
bedmethyl
methylation
updated 19 hours ago by
GenoMax
141k • written 23 hours ago by
njornet
▴ 20
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome
PCA
batch-effect
SNP
updated 13 hours ago by
Ram
43k • written 4.7 years ago by
Ace
▴ 90
1
vote
1
reply
146
views
Retrieve a % coverage for each transcript
RNA-seq
updated 14 hours ago by
Ram
43k • written 14 hours ago by
jammydodger123456
▴ 40
0
votes
1
reply
823
views
How to compare differentially expressed genes among different affymatrix dataset
microarray
batch-effect
R
updated 13 hours ago by
Ram
43k • written 4.8 years ago by
Calangoa
▴ 30
0
votes
1
reply
119
views
Freyja plot error
Freyja
updated 16 hours ago by
Ram
43k • written 21 hours ago by
Adyasha
• 0
0
votes
1
reply
157
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
updated 13 hours ago by
GenoMax
141k • written 13 hours ago by
Kai Xin
• 0
0
votes
1
reply
129
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 19 hours ago by
DKA
▴ 40 • written 21 hours ago by
james.melhorn
• 0
0
votes
1
reply
146
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 10 hours ago by
GenoMax
141k • written 10 hours ago by
ycts
• 0
0
votes
1
reply
2.7k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 11 hours ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 13 hours ago by
Ram
43k • written 6.0 years ago by
Jun
• 0
0
votes
1
reply
194
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
updated 14 hours ago by
bk11
★ 2.3k • written 1 day ago by
航太郎
• 0
0
votes
0
replies
6
views
How to root an unrooted tree with known root tree?
phylogenetics
rooting
R
5 minutes ago by
P.
• 0
0
votes
0
replies
133
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
18 hours ago by
Ronin
• 0
0
votes
0
replies
85
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 14 hours ago by
GenoMax
141k • written 15 hours ago by
srimmer
• 0
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect
scRNA-seq
feature-selection
updated 13 hours ago by
Ram
43k • written 4.9 years ago by
Lucy
▴ 140
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA
RNA-Seq
seurat
batch-effect
updated 13 hours ago by
Ram
43k • written 5.1 years ago by
akivab2
▴ 110
0
votes
0
replies
84
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 12 hours ago by
Ram
43k • written 12 hours ago by
otieno43
▴ 20
0
votes
0
replies
65
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
8 hours ago by
synat.keam
▴ 100
0
votes
0
replies
64
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
6 hours ago by
renan.igor
• 0
0
votes
0
replies
25
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
2 hours ago by
ekirsch
• 0
0
votes
0
replies
84
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
23 hours ago by
chemokine-1
▴ 10
35 results • Page
1 of 1
Recent Votes
High fold change values
C: Bcftools Mpileup Removes Marked Duplicates?
Prediction tools summary - zero values
A: Error with Formatdb of legacy blast?
Error with Formatdb of legacy blast?
Answer: How to convert SAM/BAM file to GTF/GFF file?
A: Ribo-seq vs RNA-seq read count
Recent Locations •
All
Belgium,
just now
Germany,
1 minute ago
South Korea,
4 minutes ago
South Korea,
4 minutes ago
Spain,
6 minutes ago
Singapore,
7 minutes ago
France,
9 minutes ago
Recent Awards •
All
Student
to
manaswiniparija3
▴ 40
Popular Question
to
tomas4482
▴ 390
Popular Question
to
vinayjrao
▴ 250
Scholar
to
Scooter
▴ 280
Popular Question
to
Yingying
• 0
Popular Question
to
anasjamshed
▴ 120
Popular Question
to
synat.keam
▴ 100
Recent Replies
Comment: How to reduce the variation of CIBERSORTx results?
by
feather-W
• 0
Hi LChart, Thanks for your reply. I see S-mode in the CIBERSORTx official website tutorial(https://cibersortx.stanford.edu/), and the imag…
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
First time I've heard of S-mode. I imagine you've seen this benchmark where it doesn't come out too well: https://academic.oup.com/bib/arti…
Comment: ISCN annotation for SV/CN VCF files
by
adedare
• 0
https://res.saletool.cn/vcf/18084521725806
Comment: ISCN annotation for SV/CN VCF files
by
adedare
• 0
https://res.saletool.cn/vcf/18084435127462
Comment: How can I solve this error?
by
22211020193
• 0
I want to conduct GWAS meta-analysis using metal software.
Comment: How to reduce the variation of CIBERSORTx results?
by
feather-W
• 0
Hi LChart, Thanks for your reply. Yes, the identical command lines produce different results in CIBERSORTx S-mode. Although I input the da…
Comment: Removing duplicates
by
joe
▴ 490
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates
by
samuel.a.odonnell
▴ 510
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
Answer: Pediococcus acidilactici sequence analysis
by
geneontologyhelp
▴ 340
If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data?
by
etiennedanis
▴ 10
I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates
by
joe
▴ 490
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together?
by
GenoMax
141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
swbarnes2
14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates
by
quentinperriere
• 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
Traffic: 2431 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6