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90 results • Page
1 of 2
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Votes
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0
votes
0
replies
1
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Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway.
denvo
just now by
mathavanbioinfo
▴ 90
0
votes
0
replies
13
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
30 minutes ago by
elisheva
▴ 120
3
votes
4
replies
3.9k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 5 hours ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.4k
0
votes
3
replies
114
views
RNA seq analysis
DESeq
RNA-seq
analysis
updated just now by
ATpoint
82k • written 5 hours ago by
prifa
• 0
0
votes
0
replies
68
views
Chance for trained without experience
bio
updated 5 hours ago by
ATpoint
82k • written 6 hours ago by
shehab
• 0
0
votes
0
replies
53
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
7 hours ago by
Omics data mining
▴ 260
0
votes
2
replies
103
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
6 hours ago by
njornet
▴ 20
0
votes
2
replies
100
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 49 minutes ago by
Adam
▴ 30 • written 8 hours ago by
Darya
• 0
0
votes
5
replies
164
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
68
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
0
replies
49
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
61
views
meffil.snp.concordance
meffil
methylation
snp_concordance
16 hours ago by
kyj222637
• 0
0
votes
1
reply
76
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 2 hours ago by
Bastien Hervé
5.3k • written 17 hours ago by
sooni
▴ 20
0
votes
2
replies
135
views
STAR aligner error
RNA-seq
STAR
slurm
8 hours ago by
M.
▴ 30
0
votes
0
replies
67
views
monocle 3-- Could not get node in small cluster
monocle3
19 hours ago by
synat.keam
▴ 100
0
votes
2
replies
123
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
2 hours ago by
Nicholas
• 0
0
votes
3
replies
214
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
1
reply
113
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Sony
▴ 10
5
votes
5
replies
237
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
14 hours ago by
Chris
▴ 280
0
votes
2
replies
123
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 10 minutes ago by
swbarnes2
14k • written 1 day ago by
ahmad.sajad4541
• 0
1
vote
5
replies
184
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
135
views
student
epitranscriptomics
updated 1 day ago by
ATpoint
82k • written 1 day ago by
useriwa
• 0
0
votes
0
replies
91
views
Imputation of missing genotypes
panel
beagle
imputation
1 day ago by
analyst
▴ 50
0
votes
3
replies
151
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
115
views
Correlation Analysis
statistics
methylation
NGS
expression
updated 6 hours ago by
manaswwm
▴ 510 • written 1 day ago by
Researcher
▴ 30
1
vote
2
replies
159
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
1 day ago by
robert.flynn.21
• 0
0
votes
0
replies
102
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
1 day ago by
Scott McKay
▴ 30
0
votes
0
replies
99
views
Cellphonedb results
cpdb
visulization
cellphonedb
1 day ago by
piotto
▴ 20
0
votes
0
replies
106
views
Cox Model with interaction item interpretation
Cox
2 days ago by
Bine
▴ 60
0
votes
0
replies
92
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
2 days ago by
Javier
• 0
1
vote
7
replies
442
views
Question regarding WGCNA
WGCNA
Network-construction
2 hours ago by
deepak
• 0
0
votes
0
replies
100
views
vdjtools
vdjtools
2 days ago by
yueli7
▴ 250
0
votes
1
reply
189
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 1 day ago by
andres.firrincieli
3.6k • written 2 days ago by
Antonio
• 0
0
votes
0
replies
110
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 2 days ago by
Ram
43k • written 2 days ago by
sidrah.maryam
▴ 50
0
votes
0
replies
97
views
Normalizing AMR gene count data
abundance
RGI
updated 2 days ago by
Ram
43k • written 2 days ago by
arshad1292
▴ 100
0
votes
0
replies
108
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
sarumonsus
• 0
0
votes
0
replies
113
views
How to implement an IGV to streamlit app?
python
streamlit
igv
2 days ago by
avigail.shnaider
• 0
0
votes
0
replies
122
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
3 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
112
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
3 days ago by
Christopher
• 0
0
votes
0
replies
114
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
3 days ago by
DGTool
• 0
0
votes
1
reply
182
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 1 day ago by
bk11
★ 2.4k • written 3 days ago by
Yoosef
▴ 60
0
votes
1
reply
257
views
creating batch colum for batch correction
batch-correction
combat
2 days ago by
Expert
▴ 10
0
votes
1
reply
213
views
Help with DGEList function
DGEList
R
updated 2 days ago by
marco.barr
▴ 90 • written 4 days ago by
Natali
• 0
0
votes
0
replies
152
views
Homer motif analysis
Homer
4 days ago by
daffodil
▴ 10
0
votes
1
reply
199
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Ximena
• 0
0
votes
1
reply
194
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 4 days ago by
Ram
43k • written 4 days ago by
Valentina
• 0
0
votes
6
replies
422
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
Erina
• 0
1
vote
3
replies
281
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
3 days ago by
Lada
▴ 30
1
vote
0
replies
146
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 2 days ago by
zx8754
11k • written 5 days ago by
Emilie
▴ 10
0
votes
0
replies
137
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
5 days ago by
Javier
• 0
90 results • Page
1 of 2
Recent Votes
C: salmon quantification vs. star mapping
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
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
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?
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