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1,000 results • Page
5 of 20
Sort: Views
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Views
Votes
Replies
3
votes
5
replies
1.8k
views
Limma/edgeR Design matrix for gender effect
RNA-Seq
batch-effect
updated 16 days ago by
Ram
43k • written 4.7 years ago by
kailsen
• 0
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva
batch-effect
RRBS
updated 16 days ago by
Ram
43k • written 7.2 years ago by
mrodrigues.fernanda
▴ 50
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 16 days ago by
Ram
43k • written 3.0 years ago by
Mat
▴ 60
1
vote
3
replies
1.8k
views
Using Nanoplot to asses quality of ONT data
ONT
Long-read-sequencing
NanoPlot
updated 28 days ago by
Ram
43k • written 2.3 years ago by
matt81rd
▴ 10
2
votes
2
replies
1.8k
views
EdgeR in Galaxy. Adjust C-value?
Differential-gene-expression
EdgeR
Galaxy
C-value
updated 24 days ago by
Ram
43k • written 7.6 years ago by
ando.kelli
▴ 60
0
votes
0
replies
1.8k
views
Differential expression using Scran batch corrected data
single-cell
Batch-effect
RNA-Seq
Scran
updated 15 days ago by
Ram
43k • written 5.5 years ago by
baldissera152
▴ 10
0
votes
0
replies
1.8k
views
Accounting for hidden batch effects in differential expression analysis with DEXseq and Slueth
Batch-effect
RNA-Seq
Differential-Expression
updated 16 days ago by
Ram
43k • written 7.2 years ago by
vakul.mohanty
▴ 270
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma
Batch-effect
MDS
Galaxy
updated 16 days ago by
Ram
43k • written 4.8 years ago by
sonayuv
• 0
2
votes
2
replies
1.7k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 3 hours ago by
e.r.zakiev
▴ 210 • written 3.8 years ago by
n.anuragsharma
▴ 40
1
vote
1
reply
1.7k
views
sea corrected expression matrix
sva
microarrays
batch-effect
updated 16 days ago by
Ram
43k • written 6.8 years ago by
ATCG
▴ 380
2
votes
2
replies
1.7k
views
Remove batch effect for many RNA-seq
ComBat
RNA-Seq
batch-effect
sva
updated 16 days ago by
Ram
43k • written 4.8 years ago by
Shaway
• 0
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq
Differential-Expression
batch-effect
updated 15 days ago by
Ram
43k • written 5.1 years ago by
georgians
▴ 50
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 16 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
0
votes
0
replies
1.7k
views
Differential Gene Expression Analysis using two distinct scRNA-seq datasets
differential-gene-expression
RNA-Seq
scRNA-seq
updated 24 days ago by
Ram
43k • written 6.5 years ago by
Eskimo
▴ 120
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA
RNA-Seq
seurat
batch-effect
updated 16 days ago by
Ram
43k • written 5.1 years ago by
akivab2
▴ 110
2
votes
2
replies
1.7k
views
How to add a title to a cnetplot?
r
cnetplot
updated 16 days ago by
Ram
43k • written 3.5 years ago by
appropiate
▴ 80
0
votes
5
replies
1.7k
views
what does mean this error ? "(ERR): hisat2-align exited with value 1" in mapping long noncoding RNAs
long-non-coding-RNA
lncRNA
updated 28 days ago by
Ram
43k • written 2.7 years ago by
reza
• 0
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads
RNA-seq
gene-expression
read-count
updated 28 days ago by
Ram
43k • written 2.9 years ago by
gat
• 0
0
votes
1
reply
1.6k
views
RRBS data analysis using RnBeads give Scan() error
RRBS
450k
RnBeads
updated 16 days ago by
Ram
43k • written 6.8 years ago by
rahel14350
▴ 40
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 15 days ago by
Ram
43k • written 7.3 years ago by
tolgaturant
▴ 20
0
votes
1
reply
1.6k
views
Public RNA-Seq and Microarray samples from same tissue
Microarray
RNA-Seq
Batch-Effect
updated 16 days ago by
Ram
43k • written 7.9 years ago by
Ar
★ 1.1k
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 18 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 15 days ago by
Ram
43k • written 5.0 years ago by
borkk
▴ 140
0
votes
1
reply
1.6k
views
Extraction of batch subject sequence from Blast result.
minus-strand
blastdbcmd
updated 16 days ago by
Ram
43k • written 5.9 years ago by
kabir.deb
▴ 80
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq
edgeR
batch-effect
updated 18 days ago by
Ram
43k • written 3.9 years ago by
avino
▴ 20
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq
edgeR
DESeq2
Batch-Effect
updated 16 days ago by
Ram
43k • written 5.2 years ago by
Behram Radmanesh
▴ 40
3
votes
6
replies
1.5k
views
edgeR FDR always 1
FDR
differential-gene-expression
edgeR
miRNA
updated 24 days ago by
Ram
43k • written 4.9 years ago by
AngAdd
▴ 20
1
vote
5
replies
1.5k
views
How to correct unknown Batch effect?
PCA
gene-expression
DESeq2
RNA-seq
batch-effect
updated 16 days ago by
Ram
43k • written 12 months ago by
luffy
▴ 110
2
votes
3
replies
1.5k
views
Duplicate row name not allowed while reading the file in R
RNA-Seq
deseq2
Differential-Gene-expression
R
updated 24 days ago by
Ram
43k • written 4.9 years ago by
imanbh
• 0
0
votes
0
replies
1.5k
views
RIPSeeker viewRIP function fails to extract values() in GRangesList/S4 object
RIPSeq
S4
RIP
R
updated 16 days ago by
Ram
43k • written 6.2 years ago by
CrisMar
▴ 80
0
votes
0
replies
1.5k
views
minifi for RRBS
rrbs
batch-effect
methylation
updated 16 days ago by
Ram
43k • written 7.2 years ago by
German.M.Demidov
★ 2.9k
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq
quantification
alignment
updated 16 days ago by
Ram
43k • written 5.2 years ago by
mohammedtoufiq91
▴ 250
2
votes
3
replies
1.5k
views
RNASeq - How to compare the expression of a single gene across batches
RNA-Seq
edgeR
batch-effect
updated 15 days ago by
Ram
43k • written 3.6 years ago by
oakhamwolf
▴ 20
5
votes
13
replies
1.5k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 13 days ago by
ATpoint
82k • written 14 days ago by
BioinfGuru
★ 1.7k
7
votes
7
replies
1.5k
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 18 days ago by
Dunois
★ 2.5k • written 18 days ago by
AdviceSeeker
• 0
4
votes
6
replies
1.5k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3
GenomicRanges
ORFik
GenomicFeatures
updated 18 days ago by
GenoMax
142k • written 15 months ago by
Estefania
▴ 30
0
votes
1
reply
1.5k
views
Assembled genome a little larger than Kmergeneie prediction?
kmergenie
genome-size
updated 16 days ago by
Ram
43k • written 8.1 years ago by
gerrychang1985
▴ 40
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 15 days ago by
Ram
43k • written 18 months ago by
Dominique
• 0
0
votes
0
replies
1.4k
views
Help with Circos plot "Assumption Error" that prevents plotting a protein interactions network
CircosPlot
updated 16 days ago by
Ram
43k • written 3.4 years ago by
hniels01
• 0
1
vote
2
replies
1.4k
views
gdc-client command line error
line
GDC
TCGA
command
updated 29 days ago by
yahn
• 0 • written 20 months ago by
apronstring
• 0
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq
batch-effect
deseq
updated 15 days ago by
Ram
43k • written 2.3 years ago by
claysandel
• 0
3
votes
5
replies
1.4k
views
Removing Batch effect that is the same as condition - DESEq2
RNA-Seq
batch-effect
DESeq2
updated 25 days ago by
Ram
43k • written 3.9 years ago by
annamariabugaj
• 0
1
vote
2
replies
1.4k
views
How to download a list pdb codes contained in a csv file using
Biopython
updated 16 days ago by
Ram
43k • written 3.2 years ago by
jmungar2
▴ 10
7
votes
4
replies
1.4k
views
Is there any journal article to reference removeBatchEffect function from Limma?
batch
removebatcheffect
limma
rna-seq
batch-effect
updated 16 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
0
votes
2
replies
1.4k
views
How to do a pairwise alignment and convert the result to a VCF file?
VCF
Genomics
mutations
updated 29 days ago by
johnston.mike.j
▴ 40 • written 3.0 years ago by
arturo.marin
▴ 20
2
votes
5
replies
1.4k
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
RNA-seq
Limma
Differential-gene-Expression
R
updated 24 days ago by
Ram
43k • written 23 months ago by
dzisis1986
▴ 70
0
votes
2
replies
1.4k
views
Interpretation problem at PCA plot for detecting batch effect
PCA
RNA-Seq
batch-effect
updated 16 days ago by
Ram
43k • written 4.4 years ago by
modarzi
▴ 170
1
vote
4
replies
1.4k
views
Splitting long reads into shorter chunks
long-read
updated 28 days ago by
Ram
43k • written 5.8 years ago by
pennakiza
▴ 60
1
vote
4
replies
1.3k
views
Comparing RNA-Seq data to online databases
RNA-Seq
batch-effect
updated 16 days ago by
Ram
43k • written 4.7 years ago by
Victoria
▴ 10
3
votes
5
replies
1.3k
views
NextGen Sequencing Folks, what do you keep as your raw backup? BCL's or FASTQ's? Both?
next-gen-sequencing
backups
data-storage
updated 28 days ago by
Ram
43k • written 2.2 years ago by
msn
▴ 130
1,000 results • Page
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Comment: No INFO/info value in headers
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
Greatly speed up conda by using mamba
Comment: Converting CRAM to FastQ
Parametric or non-parametric tests for qPCR significance testing between treatments?
Answer: Converting CRAM to FastQ
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Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
swbarnes2
14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
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Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme
by
e.r.zakiev
▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ
by
GenoMax
142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
Comment: Raw counts using stringtie
by
GenoMax
142k
> Error parsing strand from GFF line Looking at this error and the listing of files in your directory it looks like you need to `gunzip` t…
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