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45 results • Page
1 of 1
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Votes
Replies
0
votes
4
replies
241
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
52 minutes ago by
schmince
• 0
0
votes
1
reply
40
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
just now by
Prawesh
• 0
0
votes
9
replies
1.4k
views
kinannote software installation problems
kinannote
updated 1 hour ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
0
votes
1
reply
58
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 1 hour ago by
marco.barr
▴ 90 • written 4 hours ago by
elisheva
▴ 120
0
votes
0
replies
25
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 36 minutes ago by
Ram
43k • written 4 hours ago by
mathavanbioinfo
▴ 90
0
votes
1
reply
163
views
Seurat V5 integration
Seurat
integration
updated 30 minutes ago by
Ram
43k • written 3 days ago by
starswillfade
▴ 10
0
votes
2
replies
129
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 35 minutes ago by
Ram
43k • written 14 hours ago by
Sumeet
• 0
0
votes
0
replies
40
views
News:
Online course: Introduction to Deep Learning
Python
Deep-Learning
Convolutional-Neural-Network
Machine-Learning
updated 30 minutes ago by
Ram
43k • written 5 hours ago by
carlopecoraro2
★ 2.5k
4
votes
5
replies
3.3k
views
How to compare compare two Sam files to check mapping
alignment
updated 5 hours ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
0
votes
2
replies
79
views
How/where can I get fungal mitogenome data for analysis?
fungal
mitogenome
updated 6 hours ago by
GenoMax
142k • written 6 hours ago by
madders73
• 0
2
votes
1
reply
136
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
updated 6 hours ago by
Bastien Hervé
5.3k • written 10 hours ago by
mnx0723
• 0
3
votes
4
replies
3.9k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 9 hours ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.4k
0
votes
3
replies
161
views
RNA seq analysis
DESeq
RNA-seq
updated 1 hour ago by
Ram
43k • written 9 hours ago by
prifa
• 0
10
votes
3
replies
237
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 10 hours ago by
b.contreras.moreira
▴ 180 • written 1 day ago by
ijarne
• 0
0
votes
0
replies
82
views
Chance for trained without experience
bio
updated 10 hours ago by
ATpoint
82k • written 10 hours ago by
shehab
• 0
1
vote
2
replies
125
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
10 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
60
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
11 hours ago by
Omics data mining
▴ 260
0
votes
2
replies
116
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
10 hours ago by
njornet
▴ 20
0
votes
2
replies
127
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 4 hours ago by
Adam
▴ 30 • written 12 hours ago by
Darya
• 0
0
votes
5
replies
180
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 9 hours ago by
Joe
21k • written 12 hours ago by
Lemonhope
• 0
0
votes
0
replies
76
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
12 hours ago by
Winter
• 0
0
votes
5
replies
220
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
6 hours ago by
me
• 0
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 13 hours ago by
DGTool
• 0 • written 4.8 years ago by
ww22runner
▴ 60
2
votes
1
reply
84
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
15 hours ago by
analyst
▴ 50
0
votes
0
replies
54
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
15 hours ago by
analyst
▴ 50
0
votes
0
replies
50
views
Blog:
Introduction to The Complete Sequence of a Human Genome
biotech
15 hours ago by
usa.cd.genomics
• 0
0
votes
0
replies
55
views
Blog:
Overview of Nanopore Sequencing
biotech
15 hours ago by
usa.cd.genomics
• 0
0
votes
0
replies
66
views
meffil.snp.concordance
meffil
methylation
snp_concordance
20 hours ago by
kyj222637
• 0
0
votes
1
reply
103
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 6 hours ago by
Bastien Hervé
5.3k • written 21 hours ago by
sooni
▴ 20
1
vote
5
replies
370
views
HCL database download
HCL
updated 19 hours ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
0
votes
1
reply
219
views
barcode of TCR-sequencing
barcode
updated 22 hours ago by
mizraelson
▴ 60 • written 8 days ago by
yueli7
▴ 250
0
votes
3
replies
155
views
STAR aligner error
RNA-seq
STAR
slurm
updated 1 hour ago by
Ram
43k • written 23 hours ago by
M.
▴ 30
0
votes
0
replies
71
views
monocle 3-- Could not get node in small cluster
monocle3
23 hours ago by
synat.keam
▴ 100
0
votes
2
replies
158
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
6 hours ago by
Nicholas
• 0
0
votes
7
replies
398
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 4 hours ago by
Wayne
★ 2.0k • written 2 days ago by
JACKY
▴ 140
0
votes
2
replies
440
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 23 hours ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
5
votes
5
replies
245
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
18 hours ago by
Chris
▴ 280
0
votes
2
replies
154
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 4 hours ago by
swbarnes2
14k • written 1 day ago by
ahmad.sajad4541
• 0
2
votes
2
replies
155
views
Is therer any suggestions on mapping rate of WGBS data?
mapping
read
alignment
WGBS
18 hours ago by
Zeng Jingyu
▴ 60
0
votes
1
reply
125
views
Correlation Analysis
statistics
methylation
NGS
expression
updated 10 hours ago by
manaswwm
▴ 510 • written 1 day ago by
Researcher
▴ 30
1
vote
5
replies
306
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 12 hours ago by
Michael
54k • written 1 day ago by
qwertyuiop26
• 0
1
vote
7
replies
462
views
Question regarding WGCNA
WGCNA
Network-construction
updated 1 hour ago by
Ram
43k • written 4 days ago by
deepak
• 0
13
votes
14
replies
789
views
High Malat-1 expression in single cell data
single-cell
updated 14 hours ago by
t.montserrat.ayuso
▴ 40 • written 9 days ago by
carolofharvest
▴ 40
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 9 hours ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS
insertion site
trangene
de-novo
soap
updated 6 hours ago by
Cameron.walker9900
• 0 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
45 results • Page
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Recent Votes
removeBatchEffect explained using base R linear models
How to get number of characters (nucleotides) in fasta file
Answer: How can I analyze normalized expression data?
A: How to append the cell barcode and UMI information to the fastq header in paired
Answer: Decoding MM and ML tags in .SAM file
C: salmon quantification vs. star mapping
Answer: TFs and Gene databases
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Recent Replies
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
I probably got some of the vocabulary wrong. I thought that "Dom HOR2932 HOR3036 HOR3726 KWSBambina Rec S42IL_124" were representing my ge…
Comment: featureCounts output assigned value higher than and HISAT2 mapping.
by
Ram
43k
It's featureCount**s**, not featureCount. I've edited your post and fixed all mentions of featureCounts.
Comment: kinannote software installation problems
by
Emanoelle
• 0
Hey, I know it's been 5 years but I have the same issue. When I run the test the software is unable to perform and always deliver the follo…
Comment: STAR aligner error
by
Ram
43k
If they can't help you, we probably can't do much either. But we can optimize your STAR command. BAM SortedByCoordinate is the worst settin…
Answer: Obtaining Infinium Methylation450K manifest for hg38
by
marco.barr
▴ 90
Hi, you can check it from github here: [https://zwdzwd.github.io/InfiniumAnnotation][1]. I don't know if this is what you are looking fo…
Comment: RNA seq analysis
by
ATpoint
82k
It makes absolutely no sense to conduct such an analysis. I strongly discourage you to even start with it. Results will be utterly nonsense…
Comment: Differentail gene expression results
by
swbarnes2
14k
Cross-posted: https://support.bioconductor.org/p/9158194/
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
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