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444 results • Page
1 of 9
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0
votes
1
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30
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 1 hour ago by
andres.firrincieli
3.6k • written 2 hours ago by
kacollier
▴ 30
0
votes
0
replies
28
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
variant
3 hours ago by
ashaneev07
▴ 20
0
votes
0
replies
42
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 5 hours ago by
Ram
43k • written 6 hours ago by
curious_butterfly
• 0
0
votes
0
replies
46
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
6 hours ago by
Zeng Hao
▴ 40
0
votes
1
reply
80
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 5 hours ago by
Ram
43k • written 10 hours ago by
cput
• 0
0
votes
0
replies
57
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
10 hours ago by
asalimih
▴ 60
0
votes
4
replies
288
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
12 hours ago by
schmince
• 0
0
votes
1
reply
115
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
11 hours ago by
Prawesh
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 12 hours ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
0
votes
0
replies
56
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 11 hours ago by
Ram
43k • written 15 hours ago by
mathavanbioinfo
▴ 90
3
votes
4
replies
3.9k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 20 hours ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.4k
0
votes
3
replies
203
views
RNA seq analysis
DESeq
RNA-seq
updated 12 hours ago by
Ram
43k • written 20 hours ago by
prifa
• 0
0
votes
0
replies
103
views
Chance for trained without experience
bio
updated 21 hours ago by
ATpoint
82k • written 21 hours ago by
shehab
• 0
0
votes
0
replies
78
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
22 hours ago by
Omics data mining
▴ 260
0
votes
2
replies
134
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
21 hours ago by
njornet
▴ 20
0
votes
2
replies
161
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 15 hours ago by
Adam
▴ 30 • written 23 hours ago by
Darya
• 0
0
votes
5
replies
200
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 20 hours ago by
Joe
21k • written 23 hours ago by
Lemonhope
• 0
0
votes
0
replies
114
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
1 hour ago by
Winter
• 0
0
votes
0
replies
70
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
1 day ago by
analyst
▴ 50
0
votes
0
replies
82
views
meffil.snp.concordance
meffil
methylation
snp_concordance
1 day ago by
kyj222637
• 0
0
votes
1
reply
121
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 17 hours ago by
Bastien Hervé
5.3k • written 1 day ago by
sooni
▴ 20
0
votes
3
replies
196
views
STAR aligner error
RNA-seq
STAR
slurm
updated 12 hours ago by
Ram
43k • written 1 day ago by
M.
▴ 30
0
votes
0
replies
86
views
monocle 3-- Could not get node in small cluster
monocle3
1 day ago by
synat.keam
▴ 100
0
votes
2
replies
182
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
17 hours ago by
Nicholas
• 0
0
votes
1
reply
184
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
260
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
1 day ago by
Chris
▴ 280
0
votes
2
replies
194
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 15 hours ago by
swbarnes2
14k • written 1 day ago by
ahmad.sajad4541
• 0
1
vote
5
replies
202
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
153
views
student
epitranscriptomics
updated 1 day ago by
ATpoint
82k • written 1 day ago by
useriwa
• 0
0
votes
0
replies
103
views
Imputation of missing genotypes
panel
beagle
imputation
1 day ago by
analyst
▴ 50
0
votes
3
replies
161
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
2
replies
136
views
Correlation Analysis
statistics
methylation
NGS
expression
41 minutes ago by
Researcher
▴ 30
1
vote
2
replies
165
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
103
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
2 days ago by
Scott McKay
▴ 30
0
votes
0
replies
102
views
Cellphonedb results
cpdb
visulization
cellphonedb
2 days 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
93
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
2 days ago by
Javier
• 0
1
vote
7
replies
467
views
Question regarding WGCNA
WGCNA
Network-construction
updated 12 hours ago by
Ram
43k • written 5 days ago by
deepak
• 0
0
votes
0
replies
101
views
vdjtools
vdjtools
2 days ago by
yueli7
▴ 250
0
votes
1
reply
233
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
111
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
98
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
115
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
114
views
How to implement an IGV to streamlit app?
python
streamlit
igv
3 days ago by
avigail.shnaider
• 0
0
votes
0
replies
126
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
3 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
115
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
117
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
3 days ago by
DGTool
• 0
1
vote
2
replies
194
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
30 minutes ago by
Yoosef
▴ 60
0
votes
1
reply
258
views
creating batch colum for batch correction
batch-correction
combat
2 days ago by
Expert
▴ 10
0
votes
1
reply
215
views
Help with DGEList function
DGEList
R
updated 3 days ago by
marco.barr
▴ 90 • written 4 days ago by
Natali
• 0
444 results • Page
1 of 9
Recent Votes
Comment: Problem with Seurat package in PercentageFeatureSet function
Answer: Can I merge Hi-C fastq files from different lanes?
A: How to get SNP identifiers from VCF file?
Answer: How can I analyze normalized expression data?
Answer: How can I analyze normalized expression data?
Answer: Pruning Phylogenetic Trees and Bootstrap Values
Difference between Pysam Pileup and Fetch
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Recent Awards •
All
Popular Question
to
Gordon Smyth
★ 7.1k
Popular Question
to
kacollier
▴ 30
Popular Question
to
rackbersingh
• 0
Popular Question
to
DKA
▴ 40
Centurion
to
mathavanbioinfo
▴ 90
Popular Question
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graeme.thorn
▴ 100
Popular Question
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nhaus
▴ 360
Recent Replies
Comment: Problem with Seurat package in PercentageFeatureSet function
by
Yoosef
▴ 60
Thanks a lot for your response. Today, I finally understood what my problem was. I have used CreateAssayObject function, while I should ha…
Comment: Correlation Analysis
by
Researcher
▴ 30
there is only one value of methylation and expression per gene. I did perform corr(gene_corr$methylation_values, gene_corr$expression_value…
Answer: Enhanced Volcano-Cut off
by
marco.barr
▴ 90
from the documentation it seems that it reports limits for the value of log2 fold-change in an absolute sense. FCcutoff: Cut-off for…
Answer: Importing a fastq file
by
oumo
• 0
The fastq file is in my local disk, and I want to upload it to Ubuntu
Comment: Conda severely broken after attempting mamba install
by
andres.firrincieli
3.6k
I have been there... I just reinstalled conda.
Comment: Importing a fastq file
by
marco.barr
▴ 90
That's right.. With `cp` command from terminal cp /mnt/c/path/to/your/fastq/file.fastq /path/in/wsl/
Comment: Copy number Variation analysis using conumee
by
zylcc2
• 0
if your seqnames include "chrX" or "chrY", should add "chrXY=TRUE". like this : anno_combine <- CNV.create_anno(bin_minprobes = 15, bin_min…
Comment: Importing a fastq file
by
ATpoint
82k
Windows is mounted as `/mnt/c/...` in WSL (at least in WSL2).
Answer: Importing a fastq file
by
marco.barr
▴ 90
Can you explain better what you mean? If I understand correctly, your fastq file must be in the Ubuntu home folder of your wsl to be able t…
Answer: Seurat CellCycleScoring – confused about the proper order of operations when usi
by
Li
• 0
I‘m not an expert in sctransform or cellcyclescoring. But I think it's because sctransform creates a new assay named "SCT", which is differ…
Comment: How can I analyze normalized expression data?
by
mnx0723
• 0
thank you for comment
Comment: Pruning Phylogenetic Trees and Bootstrap Values
by
Zeng Hao
▴ 40
Dear Klaus, Thank you for the reply. If I could clarify with an example: With this tree, B0----------------- A -| B1----------…
Answer: Contig assembly task, errors
by
Philipp Bayer
8.4k
Feels a bit strange for an aptitude test, feels more like homework. 1) seems OK to me, just chuck them into CAP3 and see what falls out.…
Comment: Help with Biopython for Beginner
by
Pierre Lindenbaum
161k
Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
Answer: bcftools - reducing to "sites-only"?
by
Pierre Lindenbaum
161k
bcftools view -G in.vcf.gz <!-- Diabetic foot ulceration (DFU) is a devastating complication of diabetes whose pathogenesis rema…
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