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158 results • Page
2 of 4
Sort: Views
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Views
Votes
Replies
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
0
votes
0
replies
1.1k
views
Finding wobble/redundant positions in an RNA string using R.
RNA
wobble-position
R
updated 3 days ago by
Ram
43k • written 6.2 years ago by
fawazfebin
▴ 100
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
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
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
2
votes
6
replies
850
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 3 days ago by
Ram
43k • written 18 months ago by
JACKY
▴ 140
0
votes
0
replies
835
views
Estimating sequence complexity of DNA sequence from fasta file
sequence
RepeatMasker
pacbio
updated 3 days ago by
Ram
43k • written 5.6 years ago by
epaminonda
▴ 10
0
votes
1
reply
828
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
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
1
vote
2
replies
804
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 3 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
4
votes
13
replies
783
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 3 days ago by
BioinfGuru
★ 1.7k • written 8 days ago by
matteo.levorato
• 0
2
votes
7
replies
730
views
Removing duplicates
duplicates
ONT
minimap2
updated 1 day ago by
joe
▴ 510 • written 2 days ago by
quentinperriere
• 0
0
votes
0
replies
728
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
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
1
vote
0
replies
665
views
Conditions for valid batch effect correction
r
batch-effect
updated 3 days ago by
Ram
43k • written 5.1 years ago by
Sebastian Hesse
▴ 340
8
votes
10
replies
665
views
bash script
whole-genome-sequencing
updated 4 days ago by
Ram
43k • written 11 days ago by
bestone
▴ 30
1
vote
1
reply
655
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 3 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
2
votes
2
replies
625
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 3 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
4
votes
7
replies
527
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 6 days ago by
Ram
43k • written 7 days ago by
AHerik
▴ 20
0
votes
2
replies
520
views
autodockvina
python
python3
autodock
updated 1 day ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
0
votes
6
replies
518
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
4 days ago by
Dunois
★ 2.5k
0
votes
4
replies
512
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
21 hours ago by
Kai Xin
• 0
0
votes
4
replies
440
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
1 day ago by
feather-W
• 0
0
votes
2
replies
417
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
1 day ago by
航太郎
• 0
0
votes
1
reply
393
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 1 day ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
1
vote
4
replies
373
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 6 days ago by
BioinfGuru
★ 1.7k • written 7 days ago by
Morteza
• 0
2
votes
5
replies
362
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
2 days ago by
Bikram Kumar
• 0
0
votes
2
replies
327
views
How can I solve this error?
metal
2 days ago by
22211020193
• 0
0
votes
4
replies
322
views
Compute bootstrap values on consensus tree
phylogeny
tree
raxml
4 days ago by
pablo
▴ 300
1
vote
1
reply
320
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
10 hours ago by
renan.igor
• 0
1
vote
4
replies
315
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 6 hours ago by
Matthias Zepper
4.5k • written 8 hours ago by
Ann
★ 2.4k
1
vote
3
replies
316
views
Ensembl gene id conversion
biomart
ensembl
updated 3 days ago by
ATpoint
81k • written 5 days ago by
naveedhasan2000
• 0
0
votes
2
replies
312
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
11 hours ago by
_quantum_girl_
▴ 10
0
votes
2
replies
305
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
6 days ago by
O.rka
▴ 710
0
votes
2
replies
301
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
21 hours ago by
Ashok
• 0
0
votes
3
replies
299
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 6 days ago by
ATpoint
81k • written 8 days ago by
gdfsnkfns
• 0
0
votes
0
replies
293
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
2 days ago by
Ronin
• 0
1
vote
2
replies
293
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 4 days ago by
Istvan Albert
100k • written 5 days ago by
Jiang
• 0
0
votes
2
replies
287
views
GSEA analysis in R
GSEA
R
Arabidopsis
1 day ago by
Sudip
• 0
0
votes
2
replies
282
views
python file for coding potential calculator
cpc2.py
23 hours ago by
Ashok
• 0
2
votes
4
replies
280
views
SnpEff annotates coding duplication as intronic?
snpeff
2 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
275
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
23 hours ago by
Ashok
• 0
3
votes
2
replies
274
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
13 hours ago by
joe
▴ 510
0
votes
2
replies
264
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
3 days ago by
Koketso
• 0
1
vote
2
replies
264
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
3 days ago by
bp22
▴ 70
2
votes
2
replies
246
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
4 days ago by
bioinfo
▴ 150
0
votes
2
replies
242
views
RNAseq 1 control 2 different treatment
RNA-seq
3 days ago by
matteo.levorato
• 0
1
vote
2
replies
241
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
3 days ago by
bioinfo
▴ 150
1
vote
2
replies
239
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 2 days ago by
Ram
43k • written 2 days ago by
aniigodwinn
• 0
158 results • Page
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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
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Can you explain the normalization or give me a link that describes it, please? Comparison across samples will always be caveated as RNA-seq…
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Comment: what's the genomic location and name of gene responsible for orange and black pa
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It is not entirely off, but evidently also not correct. Melanin biosynthesis is a multistep process, that indeed prominently involves the…
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Normalized how?
Comment: Duplicate marking, read names, and the SRA
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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…
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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
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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
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>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 …
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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…
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