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370 results • Page
4 of 8
Sort: Views
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Views
Votes
Replies
0
votes
0
replies
1.3k
views
which value from ruvadj in missMethyl can present methylation status
R
RUV
methylation
missmethyl
batch-effect
updated 2 days ago by
Ram
43k • written 5.9 years ago by
RC
▴ 20
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 2 days ago by
Ram
43k • written 6.0 years ago by
Jun
• 0
1
vote
1
reply
1.3k
views
Can we use previous estimated ComBat model to correct batch effects for new data?
microarray
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 5.0 years ago by
Min Dai
▴ 160
15
votes
6
replies
1.2k
views
6 follow
VCF to human friendly form?
vcf
visualization
updated 4 days ago by
Pierre Lindenbaum
161k • written 19 months ago by
wormball
▴ 10
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 2 days ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
0
votes
2
replies
1.2k
views
Normalization (microarray data)
microarray
Normalization
Batch-effect
updated 1 day ago by
Ram
43k • written 6.3 years ago by
j_jamal96
▴ 20
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 6.7 years ago by
Dipro
• 0
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect
transcriptomics
updated 1 day ago by
Ram
43k • written 2.6 years ago by
BioQueen
▴ 30
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl
repeat
updated 4 days ago by
e.r.zakiev
▴ 200 • written 15 months ago by
liorglic
★ 1.4k
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt
R
updated 2 days ago by
Ram
43k • written 3.8 years ago by
mbk0asis
▴ 680
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome
PCA
batch-effect
SNP
updated 2 days ago by
Ram
43k • written 4.7 years ago by
Ace
▴ 90
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect
kbet
updated 1 day ago by
Ram
43k • written 4.0 years ago by
getanid123
• 0
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 2 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 1 day ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
0
votes
0
replies
1.1k
views
Extra adjustment variables during batch effect correction
rna-seq
ComBat
batch-effect
updated 2 days ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 4 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
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 2 days ago by
Ram
43k • written 4.9 years ago by
Lucy
▴ 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 1 day ago by
Ram
43k • written 5.0 years ago by
tigeradab
▴ 60
0
votes
3
replies
1.1k
views
Discrepancy between E() Values in Blastp Search - HELP
BLAST
E-value
Blastp
Protein
updated 2 days ago by
Ram
43k • written 5.3 years ago by
minasmayth
• 0
0
votes
0
replies
1.1k
views
Finding wobble/redundant positions in an RNA string using R.
RNA
wobble-position
R
updated 2 days ago by
Ram
43k • written 6.2 years ago by
fawazfebin
▴ 100
0
votes
16
replies
1.0k
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
6 days ago by
biwdpang
• 0
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva
combat
batch-effect
DESeq2
updated 2 days ago by
Ram
43k • written 3.7 years ago by
svp
▴ 680
1
vote
3
replies
1.0k
views
problem with facing strange gene name in TCGA data
TCGA
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 5.6 years ago by
modarzi
▴ 170
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 3 days ago by
Дана
• 0 • written 6 months ago by
Lukas
▴ 50
2
votes
2
replies
1.0k
views
Batch correct batch 2 while leaving batch 1 unchanged.
limma
machine-learning
batch-effect
updated 1 day ago by
Ram
43k • written 3.7 years ago by
i.sudbery
19k
3
votes
2
replies
1.0k
views
Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
RNA-Seq
Cross-Species
SVA
ComBat
Batch-Effect
updated 2 days ago by
Ram
43k • written 4.6 years ago by
rodguinea
• 0
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios
Cox-model
survival
updated 2 days ago by
Ram
43k • written 4.3 years ago by
akutasame
▴ 40
2
votes
5
replies
985
views
Ties in reranked list
fgsea
GSEA
updated 6 days ago by
Gordon
• 0 • written 6 months ago by
Hamza
• 0
2
votes
3
replies
965
views
Treating "patient" as a batch effect
ComBat_seq
DESeq2
batch-Effect
updated 2 days ago by
Ram
43k • written 17 months ago by
Mia
▴ 20
2
votes
6
replies
961
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 4 hours ago by
GenoMax
141k • written 8 months ago by
bp22
▴ 70
2
votes
2
replies
944
views
Is there a file information dictionary for files downloaded from ENCODE through batch download?
ENCODE
updated 2 days ago by
Ram
43k • written 4.6 years ago by
burcakotlu
▴ 40
2
votes
3
replies
926
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R
RNA-Seq
DE
batch-effect
GTEx
updated 4 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
2
votes
2
replies
886
views
Method to detect genome doubling
CNV
genome doubling
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 4.5 years ago by
CY
▴ 750
0
votes
0
replies
881
views
Advice on group specific condition effect and model matrix in deseq2
deseq2
batch-effect
updated 4 days ago by
Ram
43k • written 4.1 years ago by
Mozart
▴ 330
3
votes
6
replies
879
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 3.7 years ago by
oakhamwolf
▴ 20
2
votes
6
replies
848
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 2 days ago by
Ram
43k • written 18 months ago by
JACKY
▴ 140
7
votes
7
replies
844
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 4 days ago by
Dunois
★ 2.5k • written 4 days ago by
AdviceSeeker
• 0
0
votes
0
replies
835
views
Estimating sequence complexity of DNA sequence from fasta file
sequence
RepeatMasker
pacbio
updated 2 days ago by
Ram
43k • written 5.6 years ago by
epaminonda
▴ 10
0
votes
1
reply
827
views
How to compare differentially expressed genes among different affymatrix dataset
microarray
batch-effect
R
updated 2 days ago by
Ram
43k • written 4.8 years ago by
Calangoa
▴ 30
1
vote
3
replies
818
views
add INFO tag to vcf with bcftools
bcftools
vcf
updated 3 days ago by
Ram
43k • written 23 months ago by
from the mountains
▴ 230
0
votes
1
reply
812
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 1 day ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
2
replies
810
views
Is it correct to merge two raw CEL datasets and then perform quality control, background correction, and normalization on it?
R
microarray
affymetrix
batch-effect
quality-control
updated 2 days ago by
Ram
43k • written 2.8 years ago by
Sib
▴ 60
1
vote
2
replies
803
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 2 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
3
votes
2
replies
803
views
Retrieve initial query in getBM()
getBM
biomaRt
R
gene
updated 2 days ago by
Ram
43k • written 3.1 years ago by
helia.ziaei
• 0
4
votes
13
replies
778
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 2 days ago by
BioinfGuru
★ 1.7k • written 8 days ago by
matteo.levorato
• 0
11
votes
12
replies
776
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 23 hours ago by
Ram
43k • written 1 day ago by
iamsmor
• 0
0
votes
0
replies
728
views
"No group or design set" with deAna() function in EnrichmentBrowser package
RNA-Seq
R
EnrichmentBrowser
updated 2 days ago by
Ram
43k • written 4.1 years ago by
yxswhx
• 0
0
votes
0
replies
727
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
2
votes
7
replies
720
views
Removing duplicates
duplicates
ONT
minimap2
updated 22 hours ago by
joe
▴ 510 • written 2 days ago by
quentinperriere
• 0
370 results • Page
4 of 8
Recent Votes
what's the genomic location and name of gene responsible for orange and black patches in calico cats
Comment: featureCounts --primary tag counting uniquely mapped reads and excludes multi-ma
Answer: Duplicate marking, read names, and the SRA
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Answer: Cellranger count error: Input FASTQ file ended prematurely
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Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Matthias Zepper
4.5k
It is not entirely off, but evidently also not correct. Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
> so a single Rscript could utilise multiple environments and versions How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
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Normalized how?
Comment: Duplicate marking, read names, and the SRA
by
GenoMax
141k
With public data one has to work with what is there. If the information about position is absent then only thing that could be done is to l…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Or better yet. To have an R package that allows access to conda environments via "conda list env" so that environments can be switched with…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
GenoMax
141k
If GPT is right then it says that: > The specific gene responsible for the orange and non-orange (black or > gray) fur colors in cats is t…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Jean-Karim Heriche
27k
As far as I know the Orange locus hasn't been mapped to a gene. Maybe this paper will help in narrowing the search: https://www.ncbi.nlm.ni…
Comment: Duplicate marking, read names, and the SRA
by
Luka
• 0
>Curios if there a reference for this? [Apparently it's not deprecated yet][1], but will be soon and the SRA intends for it to be at some …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
I prefer RStudio for new projects as well. The moment I need versions though, RStudio becomes a burden. I wish one could launch RStudio fro…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
GenoMax
141k
According to ChatGPT: The gene responsible for the orange and black patches of fur in calico cats (and tortoiseshell cats) is the X-linked …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Certainly true. Switching versions is way simpler that way, at the cost of the familiarity of the Rstudio IDE - especially if the code is w…
Comment: Duplicate marking, read names, and the SRA
by
GenoMax
141k
> fastq-dump is deprecated Curios if there a reference for this? `fasterq-dump` seems to allow for parallel streams but `fastq-dump` is st…
Comment: Duplicate marking, read names, and the SRA
by
Luka
• 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
GenoMax
141k
To be specific, not every dataset in SRA loses the original identifiers. In many cases those remain recoverable using the `-F` option when …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
To use different versions of R and bioconductor, you don't really need RStudio. One can simply create new conda environments with the requi…
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