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246 results • Page
2 of 5
Sort: replies
Rank
Views
Votes
Replies
1
vote
5
replies
291
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
1 day ago by
anasjamshed
▴ 120
1
vote
4
replies
401
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 19 hours ago by
atowns21
• 0 • written 5 months ago by
ara
• 0
5
votes
4
replies
609
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
18 hours ago by
kirillkirilenko
▴ 40
2
votes
4
replies
236
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
15 hours ago by
samuelkalandarov2002
▴ 10
3
votes
4
replies
420
views
biomaRt error for different R version
biomaRt
R
updated 6 days ago by
GenoMax
141k • written 7 days ago by
manaswwm
▴ 490
2
votes
4
replies
263
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
21 hours ago by
HyperEvo
• 0
1
vote
4
replies
676
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 6 days ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect
transcriptomics
updated 6 days ago by
Ram
43k • written 2.6 years ago by
BioQueen
▴ 30
0
votes
4
replies
239
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
dxj294
• 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 6 days ago by
Ram
43k • written 18 months ago by
Dominique
• 0
0
votes
4
replies
512
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 4 days ago by
ATpoint
82k • written 5 days ago by
rheab1230
▴ 140
0
votes
4
replies
572
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
5 days ago by
Kai Xin
• 0
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
3
votes
4
replies
640
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
2 days ago by
rahu
• 0
0
votes
4
replies
491
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
6 days ago by
feather-W
• 0
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 6 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
5
votes
4
replies
616
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
6 days ago by
BioinfGuru
★ 1.7k
2
votes
4
replies
6.0k
views
Batch Effect Removal in RNA-Seq Data for DGE & WGCNA. Should I omit any samples according to PCA plots?
Batch-effect
RNA-Seq
R
DESeq2
updated 6 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq
batch-effect
deseq
updated 6 days ago by
Ram
43k • written 2.2 years ago by
claysandel
• 0
1
vote
4
replies
13k
views
RNA sequencing data batch effect removal
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 7.4 years ago by
Tenghui Chen
• 0
1
vote
4
replies
203
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 6 hours ago by
GenoMax
141k • written 1 day ago by
Lada
▴ 30
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq
Differential-Expression
batch-effect
updated 6 days ago by
Ram
43k • written 5.1 years ago by
georgians
▴ 50
1
vote
3
replies
3.6k
views
Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
Harmony
single-cell
scRNA-seq
batch-effect
updated 6 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
0
votes
3
replies
140
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 8 hours ago by
GenoMax
141k • written 9 hours ago by
Bertalan_Takacs
▴ 90
2
votes
3
replies
406
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
6 days ago by
valentinatsar
• 0
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 6 days ago by
Ram
43k • written 3.5 years ago by
oakhamwolf
▴ 20
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 2 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
3
replies
3.3k
views
How to correct for batch effect in microarray meta-analysis
ComBat
microarray
meta-analysis
batch-effect
updated 6 days ago by
Ram
43k • written 9.9 years ago by
BrunoGiotti
▴ 120
9
votes
3
replies
6.9k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq
edgeR
Batch-Effect
updated 6 days ago by
Ram
43k • written 9.9 years ago by
Matina
▴ 250
2
votes
3
replies
180
views
from row count to tpm
tpm
row-count
normalization
1 day ago by
michelafrancesconi9
▴ 20
3
votes
3
replies
173
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
c_u
▴ 520
5
votes
3
replies
701
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 5 days ago by
Enrique
• 0 • written 9 months ago by
Denis
▴ 310
3
votes
3
replies
461
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
joe
▴ 510
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 5 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
3
votes
3
replies
195
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Mariana
▴ 10
0
votes
3
replies
201
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 1 day ago by
Istvan Albert
100k • written 1 day ago by
Dylan
• 0
3
votes
3
replies
181
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Estevão
• 0
3
votes
3
replies
496
views
Korean human genome reference file
GWAS
reference
imputation
5 days ago by
SeoGyun
• 0
2
votes
3
replies
937
views
Method to detect genome doubling
CNV
genome doubling
updated 2 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
2
votes
3
replies
303
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 2 days ago by
dsull
★ 5.8k • written 15 days ago by
javanokendo
▴ 60
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray
Gene-expression
batch-effect
updated 6 days ago by
Ram
43k • written 6.9 years ago by
Shamim Sarhadi
▴ 220
0
votes
3
replies
359
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 1 day ago by
colindaven
6.4k • written 9 days ago by
rj.rezwan
• 0
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 6 days ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 6 days ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 6 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
1
vote
3
replies
188
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
0
votes
3
replies
191
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 1 day ago by
mchour
• 0 • written 1 day ago by
rhossen
• 0
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 6 days ago by
Ram
43k • written 7.4 years ago by
mkhadka10
• 0
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 6 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
6
votes
3
replies
161
views
Interpretting IGV output
IGV
updated 2 days ago by
Carlo Yague
8.7k • written 2 days ago by
analyst
▴ 30
246 results • Page
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Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
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Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
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Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
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I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
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I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
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Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
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by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
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Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
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We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
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