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44 results • Page
1 of 1
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0
votes
0
replies
6
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
13 minutes ago by
elisheva
▴ 120
0
votes
1
reply
136
views
Seurat V5 integration
Seurat
samples
combine
integration
updated 28 minutes ago by
Bastien Hervé
5.3k • written 3 days ago by
starswillfade
▴ 10
0
votes
2
replies
82
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 24 minutes ago by
Adam
▴ 30 • written 9 hours ago by
Sumeet
• 0
0
votes
0
replies
14
views
News:
Online course: Introduction to Deep Learning
DeepLearning
Python
ConvolutionalNeuralNetwork
MachineLearning
49 minutes ago by
carlopecoraro2
★ 2.5k
4
votes
5
replies
3.3k
views
How to compare compare two Sam files to check mapping
alignment
updated 1 hour ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
0
votes
2
replies
36
views
How/where can I get fungal mitogenome data for analysis?
fungal
mitogenome
updated 1 hour ago by
GenoMax
142k • written 1 hour ago by
madders73
• 0
1
vote
1
reply
100
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
updated 1 hour ago by
Bastien Hervé
5.3k • written 6 hours ago by
mnx0723
• 0
3
votes
4
replies
3.9k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 4 hours ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.4k
0
votes
2
replies
109
views
RNA seq analysis
DESeq
RNA-seq
analysis
3 hours ago by
prifa
• 0
10
votes
3
replies
221
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 5 hours ago by
b.contreras.moreira
▴ 180 • written 23 hours ago by
ijarne
• 0
0
votes
0
replies
66
views
Chance for trained without experience
bio
updated 5 hours ago by
ATpoint
82k • written 6 hours ago by
shehab
• 0
1
vote
2
replies
108
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
6 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
52
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
7 hours ago by
Omics data mining
▴ 260
0
votes
2
replies
101
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
5 hours ago by
njornet
▴ 20
0
votes
2
replies
97
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 29 minutes ago by
Adam
▴ 30 • written 8 hours ago by
Darya
• 0
0
votes
5
replies
160
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 4 hours ago by
Joe
21k • written 8 hours ago by
Lemonhope
• 0
0
votes
0
replies
65
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
8 hours ago by
Winter
• 0
0
votes
5
replies
185
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
2 hours ago by
me
• 0
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 9 hours ago by
DGTool
• 0 • written 4.8 years ago by
ww22runner
▴ 60
2
votes
1
reply
78
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
10 hours ago by
analyst
▴ 50
0
votes
0
replies
47
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
11 hours ago by
analyst
▴ 50
0
votes
0
replies
44
views
Blog:
Introduction to The Complete Sequence of a Human Genome
biotech
11 hours ago by
usa.cd.genomics
• 0
0
votes
0
replies
45
views
Blog:
Overview of Nanopore Sequencing
biotech
11 hours ago by
usa.cd.genomics
• 0
0
votes
0
replies
60
views
meffil.snp.concordance
meffil
methylation
snp_concordance
15 hours ago by
kyj222637
• 0
0
votes
1
reply
72
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 2 hours ago by
Bastien Hervé
5.3k • written 16 hours ago by
sooni
▴ 20
1
vote
5
replies
364
views
HCL database download
HCL
updated 15 hours ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
0
votes
1
reply
212
views
barcode of TCR-sequencing
barcode
updated 17 hours ago by
mizraelson
▴ 60 • written 8 days ago by
yueli7
▴ 250
0
votes
2
replies
133
views
STAR aligner error
RNA-seq
STAR
slurm
8 hours ago by
M.
▴ 30
0
votes
0
replies
65
views
monocle 3-- Could not get node in small cluster
monocle3
19 hours ago by
synat.keam
▴ 100
0
votes
2
replies
120
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
1 hour ago by
Nicholas
• 0
1
vote
4
replies
315
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
21 hours ago by
heelpPlease
• 0
0
votes
7
replies
367
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 30 minutes ago by
Wayne
★ 2.0k • written 1 day ago by
JACKY
▴ 140
0
votes
3
replies
212
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 21 hours ago by
Ram
43k • written 1 day ago by
schmince
• 0
0
votes
2
replies
433
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 19 hours ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
5
votes
5
replies
236
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
13 hours ago by
Chris
▴ 280
2
votes
2
replies
148
views
Is therer any suggestions on mapping rate of WGBS data?
mapping
read
alignment
WGBS
14 hours ago by
Zeng Jingyu
▴ 60
0
votes
1
reply
112
views
Correlation Analysis
statistics
methylation
NGS
expression
updated 6 hours ago by
manaswwm
▴ 510 • written 1 day ago by
Researcher
▴ 30
1
vote
5
replies
302
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 8 hours ago by
Michael
54k • written 1 day ago by
qwertyuiop26
• 0
1
vote
7
replies
442
views
Question regarding WGCNA
WGCNA
Network-construction
2 hours ago by
deepak
• 0
13
votes
14
replies
788
views
High Malat-1 expression in single cell data
single-cell
updated 10 hours ago by
t.montserrat.ayuso
▴ 40 • written 9 days ago by
carolofharvest
▴ 40
1
vote
7
replies
516
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 19 hours ago by
Chris Dean
▴ 400 • written 5 days ago by
sovrappensiero
▴ 90
0
votes
2
replies
245
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
20 hours ago by
sainavyav22
• 0
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 5 hours ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
2
votes
6
replies
2.5k
views
identifying transgene insertion site in WGS
WGS
insertion site
trangene
de-novo
soap
updated 2 hours ago by
Cameron.walker9900
• 0 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
44 results • Page
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Recent Votes
Answer: TFs and Gene databases
Answer: How can I analyze normalized expression data?
Comment: agilent human all exon sureselct v7 bed file
Answer: Best way to compare two samples in a VCF file
A: How Do Heterozygotes And Somatic Mutations Manifest In Sequencing Projects
How Do Heterozygotes And Somatic Mutations Manifest In Sequencing Projects
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Recent Replies
Answer: Seurat V5 integration
by
Bastien Hervé
5.3k
It will depend on your context and question. I guess you will want to compare gene expression between your conditions within cell types …
Answer: Error in plotting PCA plot in seurat
by
Adam
▴ 30
You get this error when you try to compare two data frames that have different dimensions. Try using the traceback() command to figure out …
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
Sorry, this was supposed to be a comment appended to the chain above. I didn't mean to post as an answer.
Comment: Exploring Diet Effects in Single-Cell RNA Sequencing
by
Adam
▴ 30
> when I looked at the expression of aging marker genes, I noticed that diets sequenced in the same batch appeared more similar. How simil…
Answer: How to compare compare two Sam files to check mapping
by
DavidStreid
▴ 90
Curious if others have also benefited from Picard's [CompareSAMs][1] tool. Seems to do exactly what Madhu has requested. If the headers …
Answer: How/where can I get fungal mitogenome data for analysis?
by
alex.zaccaron
▴ 410
The best repository is probably NCBI Organelle Resources. You can search by taxonomy and download their mt genomes. Check it out for fungi…
Answer: How/where can I get fungal mitogenome data for analysis?
by
GenoMax
142k
Good place to start looking: https://www.ncbi.nlm.nih.gov/genome/organelle/ Mitochondrial genomes may also be included in full genomes so …
Comment: Correlating Bulk Differential Expression with quantitative
by
Nicholas
• 0
Thank you! I will give it a shot
Answer: How can I analyze normalized expression data?
by
Bastien Hervé
5.3k
This has been issued a dozen times before. Have a look at Limma package. https://support.bioconductor.org/p/126817/ https://support.bioco…
Comment: Error in plotting PCA plot in seurat
by
Bastien Hervé
5.3k
Without your code, it is impossible to make any statement. Please provide the code generating that issue. By googling, here is a [similar …
Comment: A question about reference genome for creating the consensus sequence
by
me
• 0
Hi, thanks for your information. I am a bit confused now. Does this mean the cram file already contained reference genome information? I in…
Comment: PseudobulkExpression.Seurat error
by
Bastien Hervé
5.3k
> None of the requested assays are present in the object Does the assay `originalexp` exist in your object `seurat_from_cds` ?
Comment: identifying transgene insertion site in WGS
by
Cameron.walker9900
• 0
When calling for SVs using gridds, should I use the reference genome that I added my transgene to, or should I use the unedited reference?
Comment: Question regarding WGCNA
by
deepak
• 0
Thank for the reply. I am running this code: # set a set of soft-thresholding powers powers = c(c(1:20), seq(from = 22, to=30, by=2)) # Ca…
Comment: RNA seq analysis
by
prifa
• 0
thank you for your reply Zepper, a bit clarification, I took all the samples from SRA data table, but yes from different lab and also diffe…
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