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370 results • Page
2 of 8
Sort: Views
Rank
Views
Votes
Replies
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 2 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 2 days ago by
Ram
43k • written 6.3 years ago by
seta
★ 1.9k
1
vote
3
replies
3.3k
views
How to correct for batch effect in microarray meta-analysis
ComBat
microarray
meta-analysis
batch-effect
updated 1 day ago by
Ram
43k • written 9.9 years ago by
BrunoGiotti
▴ 120
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 2 days ago by
Ram
43k • written 5.2 years ago by
Davide Chicco
▴ 120
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 23 hours ago by
Ram
43k • written 7.4 years ago by
mkhadka10
• 0
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
2
votes
1
reply
3.1k
views
Batch effect correction in DE analysis of single cell RNA-seq data and visualization
Seurat
Batch-effect
SCDE
RNA-Seq
Limma
updated 2 days ago by
Ram
43k • written 5.5 years ago by
Poorya Parvizi
▴ 60
0
votes
1
reply
3.1k
views
Removing batch effects from RPKM data
limma
removeBatchEffect
batch-effect
rpkm
updated 2 days ago by
Ram
43k • written 8.5 years ago by
AB
▴ 360
0
votes
3
replies
3.0k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 23 hours ago by
Ram
43k • written 8.9 years ago by
siddharth.patel.153
• 0
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 1 day ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 23 hours ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
0
votes
2
replies
2.9k
views
Should I pre-normalize RNAseq data before combat?
RNA-Seq
combat
batch-effect
R
updated 2 days ago by
Ram
43k • written 4.8 years ago by
zhaoliang0302
▴ 50
1
vote
2
replies
2.9k
views
Taking surrogate variable into account before running PCA
sva
svaseq
batch-effect
updated 1 day ago by
Ram
43k • written 6.8 years ago by
wamiqsaifi
• 0
0
votes
1
reply
2.9k
views
Microarray batch effect correction
Microarray
Batch-effect
updated 1 day ago by
Ram
43k • written 6.6 years ago by
sarahmanderni
▴ 100
2
votes
5
replies
2.8k
views
Batch effect in Axiom Human Origins Array
affymetrix
array
batch-effect
updated 2 days ago by
Ram
43k • written 7.9 years ago by
Simo
▴ 50
0
votes
0
replies
2.8k
views
TCGA RNAseqVer2 batch effects
TCGA
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 8.5 years ago by
annadv
• 0
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA
qRT-PCR
R
targeted-assay
Batch-Effect
updated 4 days ago by
Ram
43k • written 3.9 years ago by
mohammedtoufiq91
▴ 250
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 1 day ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
1
vote
1
reply
2.8k
views
removing batch effects from large number of data sets
Microarray
batch-effect
updated 2 days ago by
Ram
43k • written 5.9 years ago by
nazaninhoseinkhan
▴ 520
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 2 days ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 2 days ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 1 day ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 2 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
0
replies
2.7k
views
Comparing lists generated by Counter() and .most_common() for AA seqs
python
amino-acid
updated 2 days ago by
Ram
43k • written 9.9 years ago by
st.ph.n
★ 2.7k
7
votes
3
replies
2.7k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 11 hours ago by
colindaven
6.3k • written 15 months ago by
Dr.Animo
▴ 130
7
votes
10
replies
2.6k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 2 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 23 hours ago by
Ram
43k • written 9.1 years ago by
chengzhao41
▴ 110
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq
batch-effect
sequencing
updated 2 days ago by
Ram
43k • written 4.6 years ago by
dmj6ab
▴ 20
0
votes
0
replies
2.6k
views
Removing batch effects from methylation beta values for molecular subtyping/cluster analysis
clustering
beta-values
batch-effect
methylation
updated 2 days ago by
Ram
43k • written 6.7 years ago by
alecmchiu
• 0
6
votes
0
replies
2.6k
views
Tool:
Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression
batch-effect
immunology
updated 23 hours ago by
Ram
43k • written 7.0 years ago by
alexis.vandenbon
▴ 80
8
votes
6
replies
2.5k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 1 day ago by
John Marshall
3.0k • written 23 months ago by
bioguy24
▴ 230
4
votes
9
replies
2.5k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 2 days ago by
Ram
43k • written 4.8 years ago by
saksis.rihards
▴ 10
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 2 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
2
votes
1
reply
2.3k
views
TCGA RNAseqV2 data matrix batch effect control and remove
RNA-Seq
batch-effect
updated 23 hours ago by
Ram
43k • written 7.6 years ago by
fractal61
▴ 10
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq
batch-effect
Random-Forest
updated 2 days ago by
Ram
43k • written 4.7 years ago by
Vlad
▴ 10
2
votes
4
replies
2.2k
views
Negative values after batch correction using removeBatchEffect from Limma
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 2 days ago by
Ram
43k • written 20 months ago by
ev97
▴ 20
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 2 days ago by
jakobjung
• 0 • written 4.6 years ago by
adhirajnath14
▴ 40
4
votes
3
replies
2.2k
views
The result of differential gene expression analysis should be extracted based on adj.p.value ?
limma
microarray
bioconductor
R
updated 2 days ago by
Ram
43k • written 6.3 years ago by
Raheleh
▴ 260
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 1 day ago by
Ram
43k • written 4.8 years ago by
BioLite
▴ 20
1
vote
0
replies
2.1k
views
Tool:
DASC -- detecting hidden batch effects in gene expression datasets (Array/RNA-Seq/scRNA-Seq)
RNA-Seq
scRNA-Seq
R
Batch-Effect
updated 23 hours ago by
Ram
43k • written 6.8 years ago by
Ar
★ 1.1k
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq
tophat
batch-effect
cufflinks
updated 2 days ago by
Ram
43k • written 5.3 years ago by
yff
• 0
1
vote
2
replies
2.1k
views
RNA-seq unbalanced batch effect correction
RNA-Seq
edgeR
R
Batch-Effect
updated 2 days ago by
Ram
43k • written 5.6 years ago by
sckinta
▴ 730
3
votes
2
replies
2.1k
views
Batch effect correction - miRNA sequencing - DESeq2
Batch-effect
DESeq2
miRNA-Seq
updated 2 days ago by
Ram
43k • written 5.4 years ago by
prekrish
• 0
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation
RNA-Seq
R
updated 2 days ago by
Ram
43k • written 6.0 years ago by
mannoulag1
▴ 120
3
votes
5
replies
2.1k
views
DE analysis with edgeR and possibly batch effect
analysis
edgeR
batch-effect
DE
updated 2 days ago by
Ram
43k • written 5.1 years ago by
seta
★ 1.9k
0
votes
5
replies
2.0k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
batch-effect
normalization
updated 2 days ago by
Ram
43k • written 20 months ago by
mmitra
▴ 60
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray
Gene-expression
batch-effect
updated 1 day ago by
Ram
43k • written 6.9 years ago by
Shamim Sarhadi
▴ 220
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect
RNA-Seq
ARSyNseq
limma
NOISeq
updated 1 day ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
0
votes
1
reply
2.0k
views
Is it appropriate to apply RUVseq on output from kallisto?
RNA-Seq
batch-correction
kallisto
updated 2 days ago by
Ram
43k • written 5.3 years ago by
unawaz
▴ 60
370 results • Page
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Recent Votes
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Comment: Installing/switching between versions of R/Rstudio/Bioconductor
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Answer: Cellranger count error: Input FASTQ file ended prematurely
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Comment: Duplicate marking, read names, and the SRA
by
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• 0
>In many cases those remain recoverable using the -F option when you dump the data (cloud download not required) The -F option (or any equ…
Answer: Duplicate marking, read names, and the SRA
by
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141k
To be specific, not every dataset in SRA loses the original identifiers. In many cases those remain recoverable using the `-F` option when …
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Done. Thank you.
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141k
Perhaps add the word linux/ubuntu to the title? You have noted that the instructions are for Ubuntu in text.
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Thanks @Ram I'll add that to the intro. I'm the admin on my machine so I haven't found it necessary to install any other way. I'll try a fr…
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No GPR files with this data unless you ask the submitters for them directly. You can find the matrix of data here: https://ftp.ncbi.nlm.nih…
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141k
That is odd. Thanks for following-up and providing an explanation.
Answer: Cellranger count error: Input FASTQ file ended prematurely
by
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▴ 70
Dear all, The reason for the error was due to the index (I1) fastq files, for example `SI-GA-A1_1_S1_L001_I1_001.fastq.gz` having a lo…
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Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
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43k
Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
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They aren't merging any datasets. Just for reference the paper is this: https://www.nature.com/articles/s41380-022-01674-9#MOESM1. Citing: …
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https://help.galaxyproject.org/
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The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
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Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
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