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395 results • Page
5 of 8
Sort: Votes
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Views
Votes
Replies
0
votes
0
replies
208
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
25 days ago by
enferdeflame
• 0
0
votes
0
replies
134
views
Modify plot R mtDNA indel
plot
mtDNA
R
10 days ago by
marco.barr
▴ 110
0
votes
1
reply
192
views
Differential Accessibility
DiffBind
updated 14 days ago by
Ram
43k • written 14 days ago by
Shloka
• 0
0
votes
1
reply
317
views
Could you please assist in identifying this cluster?
single-cell
updated 24 days ago by
Ram
43k • written 24 days ago by
carolofharvest
▴ 40
0
votes
1
reply
269
views
creating batch colum for batch correction
batch-correction
combat
7 days ago by
Expert
▴ 10
0
votes
1
reply
696
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 13 days ago by
Ram
43k • written 13 days ago by
Dr Huma Naz
• 0
0
votes
0
replies
115
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 20 days ago by
Ram
43k • written 21 days ago by
Amélie
• 0
0
votes
0
replies
222
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 24 days ago by
Ram
43k • written 24 days ago by
Dinmukhamed
• 0
0
votes
1
reply
103
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 9 hours ago by
GenoMax
142k • written 12 hours ago by
cedric.blais
• 0
0
votes
0
replies
103
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
21 days ago by
manaswwm
▴ 510
0
votes
0
replies
184
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
26 days ago by
ekirsch
• 0
0
votes
0
replies
164
views
FreeBayes detection capacity
reads
freebayes
long
29 days ago by
quentinperriere
• 0
0
votes
0
replies
218
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
17 days ago by
HarperReed
• 0
0
votes
0
replies
113
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 21 days ago by
Ram
43k • written 21 days ago by
sansan_96
▴ 90
0
votes
0
replies
188
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 17 days ago by
Ram
43k • written 18 days ago by
SineWave
• 0
0
votes
0
replies
144
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
13 days ago by
Bine
▴ 60
0
votes
3
replies
309
views
KEGG Pathways
r
RNA-seq
updated 13 days ago by
Ram
43k • written 13 days ago by
Sudip
• 0
0
votes
1
reply
200
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 20 days ago by
GenoMax
142k • written 20 days ago by
Srinka
▴ 20
0
votes
0
replies
98
views
Annotating single cell data automatically
cell
annotation
single
21 days ago by
Gerard
• 0
0
votes
4
replies
575
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
26 days ago by
feather-W
• 0
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 27 days ago by
Ram
43k • written 21 months ago by
mmitra
▴ 60
0
votes
0
replies
142
views
Chance for trained without experience
bio
updated 5 days ago by
ATpoint
82k • written 5 days ago by
shehab
• 0
0
votes
0
replies
96
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
20 days ago by
alifafiq1
• 0
0
votes
0
replies
62
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
21 hours ago by
JACKY
▴ 140
0
votes
1
reply
166
views
Provean help
variant
Provean
updated 11 days ago by
Mensur Dlakic
★ 27k • written 11 days ago by
Arun Sai Kumar
• 0
0
votes
0
replies
104
views
Use of annotation of integrated Seurat object in single sample
Seurat
11 days ago by
Bine
▴ 60
0
votes
0
replies
97
views
monocle 3-- Could not get node in small cluster
monocle3
6 days ago by
synat.keam
▴ 100
0
votes
1
reply
180
views
Microbial Signal Transduction Database
MiST
updated 4 days ago by
zx8754
11k • written 4 days ago by
Shravani
• 0
0
votes
0
replies
219
views
Lncipedia GTF file error
Proteomics
updated 24 days ago by
Ram
43k • written 25 days ago by
atharvakarkare14
▴ 30
0
votes
0
replies
151
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
16 days ago by
tnminh89
▴ 10
0
votes
1
reply
198
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 12 days ago by
i.sudbery
19k • written 13 days ago by
Edmond
• 0
0
votes
0
replies
115
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
7 days ago by
Scott McKay
▴ 30
0
votes
0
replies
1.1k
views
Finding wobble/redundant positions in an RNA string using R.
RNA
wobble-position
R
updated 27 days ago by
Ram
43k • written 6.3 years ago by
fawazfebin
▴ 100
0
votes
2
replies
362
views
GSEA analysis in R
GSEA
R
Arabidopsis
26 days ago by
Sudip
• 0
0
votes
2
replies
587
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
25 days ago by
航太郎
• 0
0
votes
0
replies
91
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
22 days ago by
sativus
▴ 20
0
votes
0
replies
154
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
10 days ago by
rustykb
▴ 20
0
votes
0
replies
183
views
what exactly is a k-mer table (remora)?
remora
basecall
27 days ago by
anne
• 0
0
votes
1
reply
177
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 3 days ago by
GenoMax
142k • written 3 days ago by
maria.soler
• 0
0
votes
0
replies
171
views
how to read graph_test output of monocle 3
monocle3
18 days ago by
synat.keam
▴ 100
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios
Cox-model
survival
updated 27 days ago by
Ram
43k • written 4.4 years ago by
akutasame
▴ 40
0
votes
0
replies
105
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
4 days ago by
Javier
• 0
0
votes
2
replies
209
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
1 day ago by
analyst
▴ 50
0
votes
0
replies
65
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
19 hours ago by
atariw
▴ 10
0
votes
2
replies
271
views
Downloading older version of a tool
Alignment
tools
10 days ago by
Ruqaiya
• 0
0
votes
0
replies
222
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 21 days ago by
Ram
43k • written 21 days ago by
Pine
▴ 20
0
votes
0
replies
96
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
22 days ago by
Biostars2200
• 0
0
votes
0
replies
122
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
8 days ago by
Christopher
• 0
0
votes
0
replies
177
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
27 days ago by
chemokine-1
▴ 10
0
votes
0
replies
214
views
miRDeep2: How to get the read counts
mirdeep2
24 days ago by
Atul K.
• 0
395 results • Page
5 of 8
Recent Votes
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
A: How can I convert -log10 (p-value) to p-value?
Comment: What does the 'E%' represent in BUSCO results?
Answer: What does the 'E%' represent in BUSCO results?
Answer: Combine Two Affymetrix Datasets With Same Platform
Comment: Kraken2 database
Comment: How does gene length effect the number of reads mapped
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Answer: Overlapping Ranges within Granges object
by
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35k
If you're not tied to Granges, you could use `bedmap --fraction-both 0.1` to require at least 10% overlap between reference and map regions…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Vijith
▴ 30
By doing some online search, I tried installing one module `cpan Bio::DB::Fasta` and it is running like a never-ending installation process…
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I have tried installing AGAT. But it failed the tests. …
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82k
That is not what the logs above tell, but good you solved it.
Answer: Inquiry about deseq2 transformation
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The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
Answer: The total expressed genes in RNA-Seq data
by
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82k
There is no robust definition of "expressed" genes, this has been asked many times before. edgeR doesn't care about "expressed", it cares (…
Answer: What is the bin size for Bamcompare?
by
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82k
It is the number of adjacent bases that are aggregated (binned) into a single value. I find binning not optimal, and would always set this …
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK
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161k
see VQSR https://gatk.broadinstitute.org/hc/en-us/articles/360035531612-Variant-Quality-Score-Recalibration-VQSR and https://gatk.broadinst…
Comment: Snakemake wrapper issue
by
Matvii Mykhailichenko
• 0
Hi, I kind of did and kind of didn't: I stopped trying to use snakemake( I remember that it's a lot of hustle to install pickard, maybe you…
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marco.barr
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Hi, you can add the labels outside chart using `geom_label_repel` from `ggrepel` package. Check out this guide [https://r-charts.com/part…
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by
Wei-Chen Pan
• 0
Hi, did you solve your problem ? I also encounter same issue but it's `wrapper:"v3.9.0/bio/picard/mergevcfs"`. In my log file, it said:…
Comment: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
No worries! I found the commit with the maths too: https://gitlab.com/ezlab/busco/-/blame/master/src/busco/busco_tools/hmmer.py?page=2#L135…
Comment: What does the 'E%' represent in BUSCO results?
by
林明德
• 0
Thank you for your answer! It really helped me resolve a doubt!
Answer: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
Ah your edit solved this. 50 BUSCOs contain internal stop codons, indicating they might be erroneous gene models, or the genes themselves a…
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by
Ashfaq
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In my case, I did not see iGPU. There is only one option, Intel UHD Graphics. What I need to do?
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