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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
1
view
Using limma in methylation EM-seq?
EM-seq
methylation
just now by
Lluís R.
★ 1.2k
0
votes
0
replies
12
views
Synteny analysis
bacterial
synteny
genome
updated 26 minutes ago by
GenoMax
141k • written 28 minutes ago by
Namil
• 0
0
votes
1
reply
21
views
Genbank File Format
gbkformat
updated 38 minutes ago by
GenoMax
141k • written 47 minutes ago by
alenew.am
• 0
0
votes
0
replies
22
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
1 hour ago by
SSSJec
• 0
0
votes
2
replies
35
views
Software to separate reads from different individuals
software
development
nanopore
10 minutes ago by
njornet
▴ 20
0
votes
0
replies
15
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
1 hour ago by
David
• 0
0
votes
2
replies
46
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 1 minute ago by
Wayne
★ 2.0k • written 2 hours ago by
Mariana
▴ 10
0
votes
0
replies
19
views
metagenomic virome quality assessment
viromics
metagenomics
and
updated 1 hour ago by
GenoMax
141k • written 2 hours ago by
Petchimuthu
• 0
0
votes
2
replies
55
views
How to update R on ubuntu
installation
update
R
apt-get
1 hour ago by
Bosberg
▴ 50
0
votes
0
replies
41
views
LEfSe
LEfSe
4 hours ago by
benkosta
• 0
0
votes
0
replies
36
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
2 hours ago by
Sara
▴ 30
0
votes
2
replies
86
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
5 hours ago by
Lluís R.
★ 1.2k
0
votes
0
replies
51
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
8 hours ago by
atharvakarkare14
▴ 10
0
votes
1
reply
77
views
What should I consider as FASTA for dataset?
PDB
FASTA
updated 3 hours ago by
GenoMax
141k • written 8 hours ago by
Nafi
• 0
0
votes
0
replies
44
views
Differential accessibility using DiffBinf
diffbind
10 hours ago by
Shloka
• 0
0
votes
0
replies
48
views
vg call vs vg surject
vg
variation
graphs
updated 3 hours ago by
GenoMax
141k • written 11 hours ago by
aliraza3119
• 0
0
votes
1
reply
71
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 3 hours ago by
GenoMax
141k • written 11 hours ago by
Winter
• 0
0
votes
1
reply
156
views
Finding batch and outlayers
Pca
updated 6 hours ago by
christopher medway
▴ 450 • written 16 hours ago by
Tigran
• 0
2
votes
2
replies
145
views
PDB related issue
rcsb
pdb
updated 16 hours ago by
noodle
▴ 570 • written 19 hours ago by
Nafi
• 0
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 10 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
0
votes
1
reply
123
views
Downloading full alignments from Pfam
pfam
updated 1 day ago by
GenoMax
141k • written 1 day ago by
bef1
• 0
0
votes
0
replies
87
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 10 minutes ago by
dariober
14k • written 1 day ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
240
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 22 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
0
votes
0
replies
111
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
1 day ago by
tnminh89
▴ 10
0
votes
0
replies
127
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
0
votes
0
replies
116
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
0
replies
498
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
2 days ago by
biocellbio
• 0
0
votes
0
replies
190
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
3 days ago by
HarperReed
• 0
1
vote
0
replies
148
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
3 days ago by
KABILAN
▴ 50
0
votes
0
replies
165
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 2 days ago by
Ram
43k • written 3 days ago by
SineWave
• 0
0
votes
0
replies
160
views
RNA-seq: full length gene
RNA-seq
updated 2 days ago by
Ram
43k • written 3 days ago by
Nargis
• 0
0
votes
0
replies
148
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
3 days ago by
turcoa1
• 0
0
votes
0
replies
155
views
Designing single-stable RNA molecules
structure
RNA
3 days ago by
Edna
• 0
0
votes
0
replies
168
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
3 days ago by
simplitia
▴ 130
0
votes
1
reply
209
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 3 days ago by
ATpoint
82k • written 3 days ago by
AaronJaime
• 0
0
votes
0
replies
164
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
3 days ago by
avocado123
• 0
0
votes
0
replies
150
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
3 days ago by
Emily
▴ 10
1
vote
0
replies
162
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
3 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
148
views
how to read graph_test output of monocle 3
monocle3
3 days ago by
synat.keam
▴ 100
0
votes
1
reply
478
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 4 days ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
146
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
4 days ago by
Aspire
▴ 300
0
votes
3
replies
280
views
Highest variable features in single cell data
single-cell
updated 2 days ago by
bk11
★ 2.4k • written 4 days ago by
Kazo
▴ 10
1
vote
3
replies
335
views
PCA plot
DESeq2
PCAplot
updated 21 hours ago by
LauferVA
4.2k • written 4 days ago by
Aaliya
▴ 10
0
votes
0
replies
145
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
4 days ago by
4fzcgueyp5
• 0
0
votes
2
replies
247
views
Annovar using R package
Annovar
gnomAD
R
3 days ago by
DKA
▴ 40
0
votes
5
replies
336
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 4 days ago by
GenoMax
141k • written 5 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
138
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 4 days ago by
Ram
43k • written 5 days ago by
glaciya2018
• 0
0
votes
0
replies
304
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
5 days ago by
pramach1
▴ 40
0
votes
1
reply
153
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 5 days ago by
Sofia
• 0 • written 5 days ago by
mawigoj318
• 0
0
votes
0
replies
139
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
5 days ago by
salias
• 0
1,000 results • Page
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Recent Votes
Answer: Mapping ortholog human and mouse transcript
C: Kallisto missing Bootstrap
Answer: Very low RNA splicing rate for pulmonary AT2 cells
Answer: what is the purpose of indexing the reference genome (Kallisto)
The Biostar Herald for Monday, April 29, 2024
The Biostar Herald for Monday, April 29, 2024
Comment: NGS forensics: how to know if data is fabricated
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★ 4.2k
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Recent Replies
Comment: Software to separate reads from different individuals
by
njornet
▴ 20
No... the extracted sample is already a mix so no way to barcode
Comment: Very low RNA splicing rate for pulmonary AT2 cells
by
e.r.zakiev
▴ 200
For anyone it might be useful: a colleague of mine, who was not dumb to use the wrong annotation `gtf`, also observed an important issue of…
Answer: Very low RNA splicing rate for pulmonary AT2 cells
by
e.r.zakiev
▴ 200
Hello people sorry I am dumb the problem lied in the fact that I had mouse cells but my `.gtf` transcriptome file was for the human. Now wi…
Comment: Genbank File Format
by
GenoMax
141k
Can you indicate if you need to do this within CLC or can use an external solution (if someone provides it here). If you need to do this in…
Comment: Downsampling fastq file
by
Ram
43k
The file being PE should not matter. I'd recommend you open an issue on the seqtk github repo as this is starting to look like some sort of…
Comment: CWl and toil singularity image e.g busybox? Thank you
by
Ram
43k
Do the developers of toil mention biostars? Where do they direct their support requests to?
Comment: How should I make kallisto indexes?
by
dsull
★ 5.9k
As an additional note, all those ``--include-attribute`` stuff was basically to restrict the transcriptome to precisely the items that Cell…
Answer: How should I make kallisto indexes?
by
dsull
★ 5.9k
I recommend the ``kb ref`` method for two reasons: 1. The index created will yield more accurate mapping for datasets that have a substa…
Comment: Software to separate reads from different individuals
by
GenoMax
141k
Were these samples barcoded when they were run. If not then you won't be able to do much.
Comment: ScRNA data question
by
bk11
★ 2.4k
The approach you are using here is the old method. Seurat is updated to V5. Please try Seurat V5 integrative analysis described in the link…
Answer: How should I make kallisto indexes?
by
Bajaj
• 0
Hi, you can still use `kallisto index -i transcripts.index transcripts.fa` (extract the gz file) for making index files. I have tried it an…
Comment: How to update R on ubuntu
by
Bosberg
▴ 50
Thanks for the suggestion, but I get several lines of results (see below) and although there are directories called `"R"`, I can't find any…
Comment: High Malat-1 expression in single cell data
by
dsull
★ 5.9k
Malat1 is a lncRNA abundant in the nucleus. I guess if Malat1 is abundant and stable, makes sense it could be detect in high amounts in scR…
Comment: CWl and toil singularity image e.g busybox? Thank you
by
Fadi
• 0
Where can I ask this question? Apparently this the place where you can help for toil?
Comment: Limma Analysis Agilent Microarray Data (GPL1708)
by
hagl
▴ 10
Dear Gordon, excuse me for not being specific regarding your advice. What would be the best way if I wanted to add new annotations to the …
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