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246 results • Page
3 of 5
Sort: replies
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Views
Votes
Replies
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 6 days ago by
Ram
43k • written 7.4 years ago by
mkhadka10
• 0
1
vote
3
replies
225
views
some error in building kraken2 database
metagenome
kraken2
1 day ago by
Art1ess
• 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 6 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray
Gene-expression
batch-effect
updated 6 days ago by
Ram
43k • written 6.9 years ago by
Shamim Sarhadi
▴ 220
9
votes
3
replies
6.9k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq
edgeR
Batch-Effect
updated 6 days ago by
Ram
43k • written 9.9 years ago by
Matina
▴ 250
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 6 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
2
replies
140
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 8 hours ago by
Ram
43k • written 17 hours ago by
sehriban.buyukkilic
▴ 10
2
votes
2
replies
401
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 1 day ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 6 days ago by
Ram
43k • written 9.1 years ago by
chengzhao41
▴ 110
0
votes
2
replies
536
views
autodockvina
python
python3
autodock
updated 6 days ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
0
votes
2
replies
177
views
Result of running of p3_in.pl
primer3
updated 2 days ago by
GenoMax
141k • written 3 days ago by
nasri
• 0
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 6 days ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
0
votes
2
replies
251
views
bam merging for archaic samples
samtools
bam
updated 3 days ago by
Ram
43k • written 4 days ago by
Matteo Ungaro
▴ 100
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 4 hours ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
7
votes
2
replies
221
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
geneontologyhelp
▴ 390 • written 2 days ago by
catherine.teyssier
• 0
0
votes
2
replies
172
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
14 hours ago by
mropri
▴ 150
0
votes
2
replies
311
views
GSEA analysis in R
GSEA
R
Arabidopsis
6 days ago by
Sudip
• 0
1
vote
2
replies
2.9k
views
Taking surrogate variable into account before running PCA
sva
svaseq
batch-effect
updated 6 days ago by
Ram
43k • written 6.9 years ago by
wamiqsaifi
• 0
3
votes
2
replies
259
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
2 days ago by
kristiewyleung
• 0
2
votes
2
replies
156
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 22 hours ago by
analyst
▴ 30 • written 1 day ago by
lorena9132
• 0
0
votes
2
replies
540
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 35 minutes ago by
Dateline
• 0 • written 21 months ago by
JZX
• 0
0
votes
2
replies
370
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
5 days ago by
Ashok
• 0
2
votes
2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray
combat
batch-effect
updated 6 days ago by
Ram
43k • written 6.7 years ago by
tleona3
▴ 10
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 6 days ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
0
votes
2
replies
176
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
Patadu94
• 0
1
vote
2
replies
226
views
permutation test in edgeR
rna-seq
edgeR
updated 2 days ago by
Gordon Smyth
★ 7.0k • written 16 days ago by
Netanel
• 0
0
votes
2
replies
409
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
5 days ago by
Ashok
• 0
2
votes
2
replies
1.6k
views
Combining control samples from 2 separate studies. Model matrix for batch effect?
gene-expression
R
limma
batch-effect
model-matrix
updated 6 days ago by
Ram
43k • written 7.2 years ago by
tolgaturant
▴ 20
2
votes
2
replies
1.0k
views
Batch correct batch 2 while leaving batch 1 unchanged.
limma
machine-learning
batch-effect
updated 6 days ago by
Ram
43k • written 3.8 years ago by
i.sudbery
19k
0
votes
2
replies
339
views
How to add motifs in cellranger-arc reference?
gtf
scRNAseq
fasta
cellranger
updated 6 days ago by
Ehsan
• 0 • written 9 weeks ago by
bioinfo
▴ 150
0
votes
2
replies
735
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 10 hours ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
2
votes
2
replies
370
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
6 days ago by
nhaus
▴ 300
0
votes
2
replies
162
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
2 days ago by
sainavyav22
• 0
0
votes
2
replies
1.2k
views
Normalization (microarray data)
microarray
Normalization
Batch-effect
updated 6 days ago by
Ram
43k • written 6.3 years ago by
j_jamal96
▴ 20
4
votes
2
replies
311
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 6 days ago by
Juke34
8.5k • written 6 days ago by
njornet
▴ 20
0
votes
2
replies
531
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
6 days ago by
航太郎
• 0
0
votes
2
replies
196
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 8 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 5.0 years ago by
tigeradab
▴ 60
0
votes
2
replies
115
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 5 hours ago by
Mensur Dlakic
★ 27k • written 8 hours ago by
biochugs
• 0
0
votes
2
replies
417
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
5 days ago by
_quantum_girl_
▴ 10
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 6 days ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
2
votes
1
reply
2.3k
views
TCGA RNAseqV2 data matrix batch effect control and remove
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 7.6 years ago by
fractal61
▴ 10
1
vote
1
reply
152
views
Failed kmer content
kmer
illumina
ngs
updated 1 day ago by
Ram
43k • written 1 day ago by
Kasturi
• 0
0
votes
1
reply
119
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
Susmita Mandal
▴ 110
1
vote
1
reply
367
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
6 days ago by
otieno43
▴ 30
1
vote
1
reply
410
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 6 days ago by
Chris
▴ 260
0
votes
1
reply
127
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
alphaflylizard
• 0
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 6 days ago by
Ram
43k • written 4.8 years ago by
BioLite
▴ 20
1
vote
1
reply
117
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 1 day ago by
GenoMax
141k • written 1 day ago by
heelpPlease
• 0
2
votes
1
reply
171
views
Seurat merge and batch correction
Seurat
updated 1 day ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
246 results • Page
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Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
by
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So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
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Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
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You will have to elaborate on what is the error
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You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
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I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
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It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
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Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
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@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
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