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34 results • Page
1 of 1
Sort: Votes
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Views
Votes
Replies
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 20 hours ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 20 hours ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
2
votes
6
replies
525
views
Removing duplicates
duplicates
ONT
minimap2
5 hours ago by
quentinperriere
• 0
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq
batch-effect
Random-Forest
updated 20 hours ago by
Ram
43k • written 4.7 years ago by
Vlad
▴ 10
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 20 hours ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
1
reply
165
views
Retrieve a % coverage for each transcript
RNA-seq
updated 21 hours ago by
Ram
43k • written 21 hours ago by
jammydodger123456
▴ 40
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 20 hours ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
1
vote
2
replies
198
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 20 hours ago by
Ram
43k • written 22 hours ago by
aniigodwinn
• 0
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 20 hours ago by
Ram
43k • written 4.8 years ago by
saksis.rihards
▴ 10
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 20 hours ago by
Ram
43k • written 6.0 years ago by
Jun
• 0
0
votes
0
replies
103
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 19 hours ago by
Ram
43k • written 19 hours ago by
otieno43
▴ 20
0
votes
1
reply
2.7k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 17 hours ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
1
reply
175
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 17 hours ago by
GenoMax
141k • written 17 hours ago by
ycts
• 0
0
votes
0
replies
86
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
15 hours ago by
synat.keam
▴ 100
0
votes
0
replies
92
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
12 hours ago by
renan.igor
• 0
0
votes
2
replies
257
views
How can I solve this error?
metal
10 hours ago by
22211020193
• 0
0
votes
0
replies
67
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
8 hours ago by
ekirsch
• 0
0
votes
4
replies
363
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
7 hours ago by
feather-W
• 0
0
votes
0
replies
61
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
6 hours ago by
P.
• 0
0
votes
0
replies
51
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau
score
tspex
6 hours ago by
bioinfo223
▴ 10
0
votes
2
replies
249
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
5 hours ago by
Kai Xin
• 0
0
votes
2
replies
245
views
GSEA analysis in R
GSEA
R
Arabidopsis
5 hours ago by
Sudip
• 0
0
votes
2
replies
163
views
RNA seq differential expression analysis
Regarding
seq
data
normalization
RNA
4 hours ago by
rrehimi
• 0
0
votes
1
reply
337
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
tree
phylogenetic
summarized
microbiome
updated 4 hours ago by
Akshay
• 0 • written 19 months ago by
Muhammad
• 0
0
votes
1
reply
134
views
Freyja plot error
Freyja
updated 22 hours ago by
Ram
43k • written 1 day ago by
Adyasha
• 0
0
votes
1
reply
90
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 1 hour ago by
GenoMax
141k • written 5 hours ago by
kirillkirilenko
▴ 20
0
votes
0
replies
100
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 21 hours ago by
GenoMax
141k • written 21 hours ago by
srimmer
• 0
0
votes
1
reply
219
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
updated 21 hours ago by
bk11
★ 2.3k • written 1 day ago by
航太郎
• 0
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome
PCA
batch-effect
SNP
updated 20 hours ago by
Ram
43k • written 4.7 years ago by
Ace
▴ 90
0
votes
4
replies
1.7k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq
batch-effect
R
updated 20 hours ago by
Ram
43k • written 4.8 years ago by
jperezboza
▴ 20
0
votes
1
reply
824
views
How to compare differentially expressed genes among different affymatrix dataset
microarray
batch-effect
R
updated 20 hours ago by
Ram
43k • written 4.8 years ago by
Calangoa
▴ 30
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 20 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 20 hours ago by
Ram
43k • written 5.1 years ago by
akivab2
▴ 110
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat
CNA
Batch-Effect
updated 20 hours ago by
Ram
43k • written 5.4 years ago by
sugus
▴ 150
34 results • Page
1 of 1
Recent Votes
Answer: Korean reference file
How to get all genes for a specific list of regions in R preferably using Biomart
Answer: differential gene expression analysis when not all samples have an untreated cou
Answer: differential gene expression analysis when not all samples have an untreated cou
Answer: Sheep reference genome remapping coordinates
Answer: Sheep reference genome remapping coordinates
DEG analysis of RNA-seq data across multiple tissues and two conditions
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Recent Replies
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Elisabeth Gasteiger
★ 2.3k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates
by
valentinatsar
• 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
Ok I made this into an answer. Could you please accept it as such.
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How to compare the quality of assemblies
by
GenoMax
141k
Are there any short read datasets available in SRA? Can you try and see how many left over reads remain after you align to both of your ass…
Comment: Korean human genome reference file
by
GenoMax
141k
From NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001712695.1/ Use the `Download` button or `curl/datasets`.
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
by
GenoMax
141k
> But it keeps giving error Please tell us what the error is.
Answer: 10x VDJ (TCR/BCR) BAM to fastq
by
GenoMax
141k
Looking at the information about the BAM file in the link included at the end of this sentence, it seems that the BAM file does not contain…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Jacky
• 0
I got it, thank you for your response.
Answer: DEseq2
by
ATpoint
81k
The DESeq2 input is a numeric count matrix (or data.frame) with rows being genes/observations and columns being samples/cells/specimen. Ple…
Comment: How to add motifs in cellranger-arc reference?
by
Ehsan
• 0
Hi. Do you have any updates on what you ended up doing? I am encountering same issue, cannot really find a good TF motif database for zebra…
Comment: biomaRt error for different R version
by
manaswwm
▴ 490
Wonderful, and thanks for tagging Mike! For those who come back for this problem, the following seemed to work for me: Downgrading `dbply…
Answer: Assume "yes" as the answer to any prompts with bioconda
by
Juke34
8.5k
From my experience using `biocontainers` base container no need to set `yes` installation is done without any command prompt, otherwise as …
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
by
Dave Carlson
★ 1.7k
You're allocating 4 compute nodes (`#SBATCH -N 4`), but STAR can't actually make use of more than 1 compute node. You can increase the num…
Answer: Assume "yes" as the answer to any prompts with bioconda
by
Dave Carlson
★ 1.7k
```conda install -y bioconda::packageX conda-forge::packageY``` should do what you're looking for.
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