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166 results • Page
3 of 4
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Views
Votes
Replies
2
votes
2
replies
187
views
PDB related issue
rcsb
pdb
updated 2 days ago by
noodle
▴ 580 • written 3 days ago by
Nafi
• 0
1
vote
1
reply
186
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 1 day ago by
Michael
54k • written 2 days ago by
Lissa Cruz Saavedra
• 0
0
votes
2
replies
185
views
What should I consider as FASTA for dataset?
PDB
FASTA
2 days ago by
Nafi
• 0
0
votes
2
replies
176
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Dora
▴ 10
1
vote
1
reply
175
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 1 day ago by
Ram
43k • written 1 day ago by
Jonathan Yoou
▴ 60
0
votes
0
replies
174
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 5 days ago by
Ram
43k • written 5 days ago by
SineWave
• 0
0
votes
0
replies
173
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
6 days ago by
simplitia
▴ 130
0
votes
2
replies
172
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
1 day ago by
matteo.levorato
• 0
0
votes
0
replies
170
views
RNA-seq: full length gene
RNA-seq
updated 5 days ago by
Ram
43k • written 5 days ago by
Nargis
• 0
0
votes
0
replies
169
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
6 days ago by
avocado123
• 0
1
vote
0
replies
168
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
6 days ago by
rohitsatyam102
▴ 850
0
votes
2
replies
167
views
How to update R on ubuntu
installation
update
R
apt-get
2 days ago by
Bosberg
▴ 50
0
votes
0
replies
163
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 6 days ago by
Ram
43k • written 6 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
163
views
Designing single-stable RNA molecules
structure
RNA
6 days ago by
Edna
• 0
0
votes
1
reply
161
views
Downloading full alignments from Pfam
pfam
updated 3 days ago by
GenoMax
141k • written 3 days ago by
bef1
• 0
2
votes
2
replies
160
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Sudip
• 0
0
votes
1
reply
158
views
Differential Accessibility
DiffBind
updated 2 days ago by
Ram
43k • written 2 days ago by
Shloka
• 0
1
vote
1
reply
157
views
Including plasmid in alignment
Bacteria
Transcriptomics
BOWTIE2
STAR
1 day ago by
heelpPlease
• 0
1
vote
0
replies
156
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
5 days ago by
KABILAN
▴ 70
0
votes
0
replies
156
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
6 days ago by
Emily
▴ 10
0
votes
0
replies
153
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
5 days ago by
turcoa1
• 0
0
votes
0
replies
153
views
how to read graph_test output of monocle 3
monocle3
6 days ago by
synat.keam
▴ 100
0
votes
1
reply
152
views
Deseq2
Deseq2
updated 1 day ago by
Jack Tierney
▴ 360 • written 1 day ago by
Sudip
• 0
0
votes
0
replies
151
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
6 days ago by
Aspire
▴ 330
0
votes
1
reply
150
views
metagenomic virome quality assessment
viromics
metagenomics
updated 2 days ago by
Ram
43k • written 2 days ago by
Petchimuthu
• 0
0
votes
0
replies
149
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
6 days ago by
4fzcgueyp5
• 0
0
votes
2
replies
141
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
2 days ago by
Lluís R.
★ 1.2k
0
votes
1
reply
137
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
updated 17 hours ago by
Ram
43k • written 20 hours ago by
rianna.collins
• 0
0
votes
0
replies
136
views
Filter low express genes in microarray data
microarray
4 days ago by
Chris
▴ 260
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
1
reply
133
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 4 hours ago by
Adam
▴ 30 • written 1 day ago by
J
• 0
0
votes
1
reply
133
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
DOBI
• 0
0
votes
1
reply
130
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 4 hours ago by
Adam
▴ 30 • written 1 day ago by
Ahiad Chen Zion
• 0
0
votes
1
reply
128
views
unable to get feature count results
featureCounts
updated 1 day ago by
Ram
43k • written 1 day ago by
Ravita
• 0
0
votes
1
reply
126
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Ruqaiya
• 0
1
vote
4
replies
119
views
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
2 hours ago by
nicole.kavanagh
• 0
0
votes
0
replies
121
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 1 day ago by
Ram
43k • written 1 day ago by
Chakri
• 0
0
votes
1
reply
120
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Winter
• 0
4
votes
0
replies
119
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
2 days ago by
Biostar
2.7k
0
votes
1
reply
118
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 11 hours ago by
i.sudbery
19k • written 22 hours ago by
Edmond
• 0
0
votes
0
replies
115
views
Synteny analysis
bacterial
synteny
genome
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Namil
• 0
0
votes
0
replies
115
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 2 days ago by
dariober
14k • written 3 days ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
113
views
Using limma in methylation EM-seq?
EM-seq
methylation
2 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
110
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
1 day ago by
Jacob
• 0
0
votes
0
replies
106
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
102
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
1 day ago by
8armed
• 0
0
votes
0
replies
102
views
Defined objects of type "S4" error in single cell analysis
Seurat
single-cell
DoubletFinder
single-nuclei
SeuratObject
1 day ago by
sarphilsar
• 0
0
votes
0
replies
98
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
1 day ago by
Bine
▴ 60
0
votes
0
replies
97
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
95
views
barcode of TCR-sequencing
barcode
1 day ago by
yueli7
▴ 250
166 results • Page
3 of 4
Recent Votes
C: TOPGO- how to do GO enrichment using a custom go database?
Answer: NGS forensics: how to know if data is fabricated
Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
Comment: DESeq2 processing problems
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
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Recent Replies
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
141k
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…
Comment: RNA editing sites based on DNA seq and RNA seq
by
Adam
▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject
by
Adam
▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems
by
Adam
▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size Can…
Answer: cnetplot category names are too long
by
bkleiboeker
▴ 370
I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
Comment: Telescope issue
by
GenoMax
141k
You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
Comment: Mutect2 for mitochondria variant discovery
by
GenoMax
141k
> I keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
Comment: Telescope issue
by
eleven11
• 0
Thank you! how would I correct that?
Comment: DESeq2 processing problems
by
Ram
43k
This is an open science community, not a place to write an email to Michael Love. Please address the entire community.
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