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153 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 3 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 1 day 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 2 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 3 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 3 days ago by
Ram
43k • written 4.1 years ago by
Mozart
▴ 330
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
0
votes
0
replies
834
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
825
views
How to compare differentially expressed genes among different affymatrix dataset
microarray
batch-effect
R
updated 1 day ago by
Ram
43k • written 4.8 years ago by
Calangoa
▴ 30
0
votes
1
reply
808
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 20 hours ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
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
4
votes
13
replies
773
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
0
votes
0
replies
727
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
726
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 20 hours ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
2
votes
7
replies
702
views
Removing duplicates
duplicates
ONT
minimap2
updated 15 hours ago by
joe
▴ 510 • written 2 days ago by
quentinperriere
• 0
1
vote
0
replies
663
views
Conditions for valid batch effect correction
r
batch-effect
updated 2 days ago by
Ram
43k • written 5.1 years ago by
Sebastian Hesse
▴ 340
8
votes
10
replies
661
views
bash script
whole-genome-sequencing
updated 3 days ago by
Ram
43k • written 11 days ago by
bestone
▴ 30
1
vote
1
reply
652
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 2 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 2 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
4
votes
7
replies
525
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 5 days ago by
Ram
43k • written 6 days ago by
AHerik
▴ 20
0
votes
2
replies
517
views
autodockvina
python
python3
autodock
updated 18 hours ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
0
votes
6
replies
513
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
3 days ago by
Dunois
★ 2.5k
0
votes
4
replies
475
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
8 hours ago by
Kai Xin
• 0
0
votes
4
replies
430
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
1 day ago by
feather-W
• 0
0
votes
1
reply
383
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
0
votes
2
replies
372
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
14 hours ago by
航太郎
• 0
0
votes
3
replies
356
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 15 hours ago by
swbarnes2
14k • written 1 day ago by
rrehimi
• 0
2
votes
5
replies
349
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
4
replies
319
views
Compute bootstrap values on consensus tree
phylogeny
tree
raxml
3 days ago by
pablo
▴ 300
0
votes
2
replies
318
views
How can I solve this error?
metal
1 day ago by
22211020193
• 0
1
vote
3
replies
312
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
301
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
5 days ago by
O.rka
▴ 710
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
1
vote
2
replies
290
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 3 days ago by
Istvan Albert
100k • written 5 days ago by
Jiang
• 0
0
votes
2
replies
285
views
GSEA analysis in R
GSEA
R
Arabidopsis
1 day ago by
Sudip
• 0
2
votes
4
replies
274
views
SnpEff annotates coding duplication as intronic?
snpeff
2 days ago by
kirill.zaslavsky
• 0
0
votes
0
replies
269
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
0
votes
2
replies
268
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 7 days ago by
Apollonia
• 0
0
votes
1
reply
268
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
updated 13 hours ago by
cmdcolin
★ 3.8k • written 1 day ago by
renan.igor
• 0
0
votes
2
replies
261
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
2 days ago by
Koketso
• 0
1
vote
2
replies
260
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
3 days ago by
bp22
▴ 60
0
votes
2
replies
257
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
6 days ago by
ramin.k2013
• 0
0
votes
2
replies
253
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
8 hours ago by
Ashok
• 0
2
votes
2
replies
245
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
3 days ago by
bioinfo
▴ 150
0
votes
2
replies
238
views
RNAseq 1 control 2 different treatment
RNA-seq
3 days ago by
matteo.levorato
• 0
1
vote
2
replies
237
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 1 day ago by
Ram
43k • written 1 day ago by
aniigodwinn
• 0
0
votes
2
replies
236
views
python file for coding potential calculator
cpc2.py
10 hours ago by
Ashok
• 0
2
votes
1
reply
236
views
VEP annotation --per_gene allele choice
VEP
updated 6 days ago by
Ram
43k • written 7 days ago by
atariw
▴ 10
1
vote
1
reply
234
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 6 days ago by
Ram
43k • written 7 days ago by
Fish
• 0
153 results • Page
2 of 4
Recent Votes
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Comment: Illumina reads preprocessing best practice for snp calling applications
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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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The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
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Thank you, I added 'accurate' now ;) I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
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I found answer https://www.biostars.org/p/101191/.
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it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
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I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
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My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
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thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably
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Kai Xin
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will look into that. Thank you very much
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