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1,000 results • Page
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
1
reply
409
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 13 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 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
0
replies
187
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
14 days ago by
P.
• 0
0
votes
0
replies
178
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
14 days ago by
ekirsch
• 0
1
vote
1
reply
466
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
12 days ago by
renan.igor
• 0
0
votes
0
replies
194
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
14 days ago by
synat.keam
▴ 100
0
votes
1
reply
290
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 14 days ago by
GenoMax
142k • written 14 days ago by
ycts
• 0
0
votes
4
replies
618
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
13 days ago by
Kai Xin
• 0
1
vote
1
reply
242
views
Retrieve a % coverage for each transcript
RNA-seq
updated 14 days ago by
Ram
43k • written 14 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
399
views
How can I solve this error?
metal
14 days ago by
22211020193
• 0
0
votes
0
replies
179
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 14 days ago by
GenoMax
142k • written 14 days ago by
srimmer
• 0
1
vote
2
replies
300
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 14 days ago by
Ram
43k • written 14 days ago by
aniigodwinn
• 0
0
votes
0
replies
364
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
14 days ago by
Ronin
• 0
2
votes
7
replies
887
views
Removing duplicates
duplicates
ONT
minimap2
updated 13 days ago by
noodle
▴ 580 • written 14 days ago by
quentinperriere
• 0
0
votes
1
reply
216
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 14 days ago by
DKA
▴ 40 • written 14 days ago by
james.melhorn
• 0
0
votes
1
reply
204
views
Freyja plot error
Freyja
updated 14 days ago by
Ram
43k • written 15 days ago by
Adyasha
• 0
0
votes
0
replies
168
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
15 days ago by
chemokine-1
▴ 10
0
votes
4
replies
543
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
14 days ago by
feather-W
• 0
0
votes
2
replies
261
views
Bedmethyl file format
bedmethyl
methylation
updated 14 days ago by
GenoMax
142k • written 15 days ago by
njornet
▴ 20
0
votes
0
replies
185
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
15 days ago by
Ali
• 0
2
votes
4
replies
345
views
SnpEff annotates coding duplication as intronic?
snpeff
15 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
276
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
14 days ago by
mropri
▴ 150
0
votes
0
replies
157
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
15 days ago by
shasabhi1
• 0
0
votes
0
replies
144
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
15 days ago by
Nishat
• 0
0
votes
0
replies
174
views
what exactly is a k-mer table (remora)?
remora
basecall
15 days ago by
anne
• 0
1
vote
1
reply
196
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 15 days ago by
dsull
★ 5.9k • written 15 days ago by
niruf
• 0
0
votes
0
replies
153
views
GWAS Phenotypes
GWAS
15 days ago by
solomoncharles77
▴ 90
0
votes
2
replies
342
views
GSEA analysis in R
GSEA
R
Arabidopsis
14 days ago by
Sudip
• 0
0
votes
0
replies
129
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
16 days ago by
QX
• 0
2
votes
5
replies
515
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
15 days ago by
Bikram Kumar
• 0
0
votes
2
replies
278
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 15 days ago by
Ram
43k • written 16 days ago by
David
• 0
1
vote
2
replies
291
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
15 days ago by
bioinfo
▴ 150
0
votes
1
reply
208
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 16 days ago by
bk11
★ 2.4k • written 16 days ago by
sinhas
• 0
0
votes
1
reply
225
views
merging Seurat objects after SCT
Seurat
SCT
updated 16 days ago by
Ram
43k • written 16 days ago by
michelle.swarovski
• 0
0
votes
1
reply
233
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 16 days ago by
GenoMax
142k • written 16 days ago by
haiying.kong
▴ 360
0
votes
2
replies
289
views
RNAseq 1 control 2 different treatment
RNA-seq
16 days ago by
matteo.levorato
• 0
1
vote
0
replies
152
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 16 days ago by
Ram
43k • written 16 days ago by
Oscar
▴ 10
2
votes
0
replies
218
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
16 days ago by
Alexander
▴ 220
1
vote
1
reply
193
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 16 days ago by
GenoMax
142k • written 16 days ago by
eesiribloom
▴ 80
0
votes
0
replies
145
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
16 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
150
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
17 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
158
views
FreeBayes detection capacity
reads
freebayes
long
17 days ago by
quentinperriere
• 0
0
votes
2
replies
274
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
14 days ago by
DKA
▴ 40
0
votes
0
replies
170
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
17 days ago by
Hien
• 0
0
votes
2
replies
308
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
15 days ago by
Koketso
• 0
0
votes
0
replies
197
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 17 days ago by
Ram
43k • written 17 days ago by
menyawino
• 0
1
vote
3
replies
373
views
Ensembl gene id conversion
biomart
ensembl
updated 16 days ago by
ATpoint
82k • written 18 days ago by
naveedhasan2000
• 0
1
vote
2
replies
332
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 16 days ago by
Istvan Albert
100k • written 18 days ago by
Jiang
• 0
0
votes
0
replies
200
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
18 days ago by
YiweiZhu
▴ 30
0
votes
2
replies
330
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
18 days ago by
O.rka
▴ 710
1,000 results • Page
4 of 20
Recent Votes
Define enhancer regions
A: how can i download human ribosomal reference ?
Answer: Bacterial plasmid analysis
Answer: Bacterial plasmid analysis
Discrepancy in read counts from fastq
R: Unable to use analyzeFeatures because argument is not a vector
Comment: Odd alignment question/finding
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Apex92
▴ 280
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
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Jeol
▴ 20
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lefthandgergo
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nicole.kavanagh
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Recent Replies
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?
by
Scooter
▴ 280
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…
Answer: Basic stats in hierfstat
by
mdav
• 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
Comment: GATK won't produce figures while analyzing covariates to generate 'recal_plots.p
by
GenoMax
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…
Comment: DESeq2 processing problems
by
ATpoint
82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot
by
LChart
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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