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129 results • Page
1 of 3
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 6 days 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 6 days ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
3
votes
3
replies
457
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 3 days ago by
swbarnes2
14k • written 5 days ago by
joe
▴ 510
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 5 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 5 days ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
2
votes
5
replies
422
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
6 days ago by
Bikram Kumar
• 0
2
votes
7
replies
799
views
Removing duplicates
duplicates
ONT
minimap2
updated 5 days ago by
joe
▴ 510 • written 6 days ago by
quentinperriere
• 0
2
votes
9
replies
733
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 4 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
2
votes
3
replies
187
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
updated 19 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
samuelkalandarov2002
▴ 10
2
votes
5
replies
412
views
Marking duplicates using UMIs
Deduplication
UMI
updated 1 day ago by
i.sudbery
19k • written 3 days ago by
Lipika
• 0
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 5 days ago by
Ram
43k • written 18 months ago by
Dominique
• 0
2
votes
5
replies
668
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 3 days ago by
Jesse
▴ 740 • written 4 days ago by
Ann
★ 2.4k
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 6 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
1
vote
2
replies
266
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 6 days ago by
Ram
43k • written 6 days ago by
aniigodwinn
• 0
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 5 days ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
1
vote
1
reply
218
views
Retrieve a % coverage for each transcript
RNA-seq
updated 6 days ago by
Ram
43k • written 6 days ago by
jammydodger123456
▴ 40
1
vote
1
reply
132
views
Failed kmer content
kmer
illumina
ngs
updated 14 hours ago by
Ram
43k • written 22 hours ago by
Kasturi
• 0
1
vote
3
replies
164
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
18 hours ago by
WouterDeCoster
47k
1
vote
2
replies
223
views
permutation test in edgeR
rna-seq
edgeR
updated 1 day ago by
Gordon Smyth
★ 7.0k • written 15 days ago by
Netanel
• 0
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 6 days ago by
Ram
43k • written 4.8 years ago by
saksis.rihards
▴ 10
1
vote
1
reply
405
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 3 days ago by
Gordon Smyth
★ 7.0k • written 5 days ago by
Chris
▴ 260
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 6 days ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
5
replies
223
views
Downsampling fastq file
downsample
fastq
updated 1 day ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 80
1
vote
1
reply
378
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
4 days ago by
renan.igor
• 0
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq
batch-effect
Random-Forest
updated 6 days ago by
Ram
43k • written 4.7 years ago by
Vlad
▴ 10
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 5 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
1
vote
0
replies
532
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
3 days ago by
mathavanbioinfo
▴ 90
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 1 day ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
0
votes
0
replies
163
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
6 days ago by
ekirsch
• 0
0
votes
2
replies
361
views
How can I solve this error?
metal
6 days ago by
22211020193
• 0
0
votes
0
replies
168
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
6 days ago by
synat.keam
▴ 100
0
votes
1
reply
261
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 6 days ago by
GenoMax
141k • written 6 days ago by
ycts
• 0
0
votes
2
replies
210
views
Bedmethyl file format
bedmethyl
methylation
updated 6 days ago by
GenoMax
141k • written 6 days ago by
njornet
▴ 20
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 6 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 6 days ago by
Ram
43k • written 6.1 years ago by
Jun
• 0
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect
kbet
updated 5 days ago by
Ram
43k • written 4.0 years ago by
getanid123
• 0
0
votes
0
replies
729
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 5 days ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat
CNA
Batch-Effect
updated 6 days ago by
Ram
43k • written 5.5 years ago by
sugus
▴ 150
0
votes
2
replies
230
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
6 days ago by
DKA
▴ 40
0
votes
0
replies
165
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
6 days ago by
Ali
• 0
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA
RNA-Seq
seurat
batch-effect
updated 6 days ago by
Ram
43k • written 5.1 years ago by
akivab2
▴ 110
0
votes
0
replies
1.9k
views
Correcting batch effect from known variables in RnBeads using Combat
Combat
450k
methylation
RnBeads
batch-effect
updated 5 days ago by
Ram
43k • written 7.1 years ago by
rahel14350
▴ 40
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 5 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
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 6 days ago by
Ram
43k • written 4.9 years ago by
Lucy
▴ 140
0
votes
0
replies
1.9k
views
batch effect in radseq
radseq
batch-effect
SNP
updated 5 days ago by
Ram
43k • written 7.5 years ago by
oselm
▴ 50
0
votes
0
replies
161
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 6 days ago by
GenoMax
141k • written 6 days ago by
srimmer
• 0
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect
RNA-Seq
ARSyNseq
limma
NOISeq
updated 5 days ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
0
votes
1
reply
815
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 5 days ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq
batch-effect
updated 5 days ago by
Ram
43k • written 6.6 years ago by
boymin2020
▴ 80
0
votes
1
reply
829
views
How to compare differentially expressed genes among different affymatrix dataset
microarray
batch-effect
R
updated 6 days ago by
Ram
43k • written 4.8 years ago by
Calangoa
▴ 30
129 results • Page
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Recent Votes
Comment: Per base sequence content error in RNAseq analysis
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
Comment: TCGA2STAT Error: Firehose connection
Answer: HaplotypeCaller - only SNPs
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Comment: How to compare the quality of assemblies
by
kirillkirilenko
▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs
by
analyst
▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
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The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
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Mensur Dlakic
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There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
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by
atowns21
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Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus
by
GenoMax
141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
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by
Art1ess
• 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
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4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
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4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs
by
Pierre Lindenbaum
161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024
by
geneontologyhelp
▴ 380
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
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