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505 results • Page
4 of 11
Sort: Votes
Rank
Views
Votes
Replies
0
votes
0
replies
49
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
14 hours ago by
meck
• 0
0
votes
0
replies
162
views
Saccharomyces cerevisiae orthologs in plants
database
orthologs
27 days ago by
dec986
▴ 370
0
votes
0
replies
332
views
How to convert dataframe properly to anndata?
single-cell
python
anndata
updated 27 days ago by
Ram
43k • written 6 months ago by
bioinfo
▴ 150
0
votes
2
replies
281
views
Regions not clear in VCF
whole-exome
variant-calling
updated 23 days ago by
Ram
43k • written 24 days ago by
priya.bmg
▴ 60
0
votes
5
replies
2.1k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
batch-effect
normalization
updated 15 days ago by
Ram
43k • written 21 months ago by
mmitra
▴ 60
0
votes
0
replies
1.8k
views
Accounting for hidden batch effects in differential expression analysis with DEXseq and Slueth
Batch-effect
RNA-Seq
Differential-Expression
updated 15 days ago by
Ram
43k • written 7.2 years ago by
vakul.mohanty
▴ 270
0
votes
0
replies
254
views
What does it means, when 2-direction perturbed pathways are identified in the gage enrichment analysis?
r
pathway
go-enrichment
gage
29 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
97
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
10 days ago by
Enrique
• 0
0
votes
1
reply
762
views
Low SNP Overlap with Michigan 1KG and TopMed reference panel
Michigan-Server
Phasing
TopMed
updated 29 days ago by
Ram
43k • written 12 months ago by
berndmann
▴ 10
0
votes
0
replies
115
views
Extracting tcga images for cnn in r
rstudio
python
tcga-lihc
svs
27 days ago by
jain72744
▴ 10
0
votes
2
replies
397
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
13 days ago by
Ashok
• 0
0
votes
0
replies
198
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 19 days ago by
Ram
43k • written 19 days ago by
roussine
▴ 10
0
votes
0
replies
96
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 8 days ago by
Ram
43k • written 9 days ago by
SSSJec
• 0
0
votes
0
replies
170
views
Problem with GATK FilterMutectCalls : using contamination table doesn' t change anything
vcf
contaminationtable
gatk
filtermutectcalls
genomics
27 days ago by
Samuel
▴ 20
0
votes
1
reply
306
views
Sheep-Human ortholog mapping with BioMart and Orthogene/Gprofiler
ortholog
sheep
updated 24 days ago by
Shuang He
• 0 • written 3 months ago by
Michael
• 0
0
votes
0
replies
167
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 13 days ago by
Ram
43k • written 14 days ago by
bioinfo223
▴ 10
0
votes
5
replies
338
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
7 days ago by
njornet
▴ 20
0
votes
0
replies
103
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 days ago by
Adyasha
• 0
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 13 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 11 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
0
votes
0
replies
134
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
4 days ago by
tnminh89
▴ 10
0
votes
0
replies
193
views
KaryoPlot: Gene coverage over centromeric regions
Gene
coverage
Centromere
Bedtools
20 days ago by
Mary
• 0
0
votes
2
replies
262
views
Annovar using R package
Annovar
gnomAD
R
6 days ago by
DKA
▴ 40
0
votes
0
replies
115
views
Variant Calling for one gene - Stage of filtering
gatk
picard
variant-calling
updated 29 days ago by
Ram
43k • written 29 days ago by
andrebolerbarros
• 0
0
votes
6
replies
482
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
22 days ago by
marongiu.luigi
▴ 710
0
votes
1
reply
223
views
Best way to add alter fastq file by adding short repeats
fastq
updated 26 days ago by
GenoMax
142k • written 26 days ago by
pairedttest
▴ 10
0
votes
0
replies
89
views
Annotating single cell data automatically
cell
annotation
single
9 days ago by
Gerard
• 0
0
votes
1
reply
170
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 8 days ago by
bk11
★ 2.4k • written 8 days ago by
alphaflylizard
• 0
0
votes
0
replies
1.2k
views
Extra adjustment variables during batch effect correction
rna-seq
ComBat
batch-effect
updated 15 days ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
0
votes
0
replies
120
views
Extracting Enhancer Regions from ENCODE Annotation Files
ENCODE
enhancer
28 days ago by
YamengWu
• 0
0
votes
0
replies
108
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 1 day ago by
Ram
43k • written 1 day ago by
Alexandros
• 0
0
votes
0
replies
259
views
help a general guideline of bioinformatics strategy to analize gut metagenome virome data from stool samples
gut-virome
updated 29 days ago by
Ram
43k • written 8 weeks ago by
Israel
• 0
0
votes
0
replies
62
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
18 hours ago by
VITALA
• 0
0
votes
0
replies
210
views
Copy number variation plot
Copy-number-variation
genomics
updated 12 days ago by
Ram
43k • written 12 days ago by
Emmi
• 0
0
votes
0
replies
169
views
Analyzing differentially methylated regions from Nanopore long read data?
Long-read-sequencing
methylation
updated 26 days ago by
Ram
43k • written 6 weeks ago by
Arton
• 0
0
votes
0
replies
214
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
9 days ago by
Javier
• 0
0
votes
2
replies
342
views
GSEA analysis in R
GSEA
R
Arabidopsis
14 days ago by
Sudip
• 0
0
votes
1
reply
659
views
How to find the co ordinates of long reads (simulated by Badreads) with respect to the reference genome
long-reads
reference-genome
assembly
updated 26 days ago by
Ram
43k • written 2.7 years ago by
Ashi
▴ 20
0
votes
0
replies
110
views
Databases with GoF (Gain of Function) annotations.
gof
lof
gain-of-function
22 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
102
views
Issue while using circle_dat function from GOplot in R
GOplot
R
21 days ago by
ckelly96
• 0
0
votes
5
replies
355
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 4 days ago by
Istvan Albert
100k • written 8 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
120
views
Installing SALSA and HIRise scafolding software
scafolding
SALSA
genome-assembly
HIRise
updated 20 days ago by
Ram
43k • written 21 days ago by
Lissa Cruz Saavedra
• 0
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 16 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect
scRNA-seq
feature-selection
updated 14 days ago by
Ram
43k • written 4.9 years ago by
Lucy
▴ 140
0
votes
0
replies
117
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
8 days ago by
Kash
▴ 110
0
votes
0
replies
88
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
9 days ago by
feather-W
• 0
0
votes
0
replies
72
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 12 hours ago by
Ram
43k • written 14 hours ago by
Oscar
▴ 10
0
votes
2
replies
280
views
bam merging for archaic samples
samtools
bam
updated 10 days ago by
Ram
43k • written 11 days ago by
Matteo Ungaro
▴ 100
0
votes
1
reply
50
views
How to perform single cell multimodal integration using Seurat for Geo datasets
cell
analysis
multimodal
single
updated 2 hours ago by
ATpoint
82k • written 3 hours ago by
nithya
• 0
0
votes
0
replies
108
views
How to extract BED-format annotation tracks for the newly inserted segments
bed
mauve
updated 29 days ago by
Ram
43k • written 29 days ago by
FZ
• 0
505 results • Page
4 of 11
Recent Votes
Answer: Bacterial plasmid analysis
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Answer: Bacterial plasmid analysis
Answer: Bacterial plasmid analysis
Discrepancy in read counts from fastq
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Answer: Subsetting and merging back Seurat Object brings different results
by
Bine
▴ 60
Noone has an idea? Thank you!
Answer: Bacterial plasmid analysis
by
shenwei356
8.5k
My colleague has an unpublished tool for plasmid analysis (clustering), and it has really good results. You might have a try. https://githu…
Comment: Odd alignment question/finding
by
ATpoint
82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
Comment: How to perform single cell multimodal integration using Seurat for Geo datasets
by
ATpoint
82k
It's funny that you ask because the paper that these data were used for is called `Integrated analysis of multimodal single-cell data` from…
Comment: Odd alignment question/finding
by
liorglic
★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
Answer: Bacterial plasmid analysis
by
Mensur Dlakic
★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
Comment: POSSUM not working due to incompatible pssm file
by
rianna.collins
• 0
Thank you so much. I'm new to this and didn't realise there was a code option.
Answer: Is there a way to increase the automatic label text size in Cytoscape?
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Greetings, Are you saying that you can't use the size setting in the style tab? That should certainly work, as should the label size se…
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Hi Zoe, did you find an answer for this? I am also getting the same error.
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142k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
Comment: Post-imputation plot
by
kl
▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis
by
GenoMax
142k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
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82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
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3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
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