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116,713 results • Page
3 of 2335
Sort: Rank
Rank
Views
Votes
Replies
3
votes
2
replies
284
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 3 days ago by
i.sudbery
19k • written 5 days ago by
vanbelj
▴ 40
0
votes
0
replies
115
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 2 days ago by
dariober
14k • written 4 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
285
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 3 days ago by
ATpoint
82k • written 4 days ago by
Francesco
▴ 10
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
138
views
Filter low express genes in microarray data
microarray
4 days ago by
Chris
▴ 260
0
votes
1
reply
323
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 days ago by
Jesse
▴ 740 • written 12 days ago by
yifangt86
▴ 60
0
votes
2
replies
338
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 4 days ago by
Jesse
▴ 740 • written 7 days ago by
Broccoli
• 0
4
votes
3
replies
349
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 4 days ago by
Arup Ghosh
3.2k • written 5 days ago by
chaco001
▴ 40
1
vote
3
replies
376
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 3 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
O.rka
▴ 710
0
votes
2
replies
249
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
5 days ago by
Guille
• 0
4
votes
2
replies
286
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
2 days ago by
pairedttest
▴ 10
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 5 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
565
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
5 days ago by
biocellbio
• 0
4
votes
8
replies
630
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 5 days ago by
Alex Reynolds
35k • written 6 days ago by
J
▴ 10
4
votes
7
replies
671
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 5 days ago by
dsull
★ 5.9k • written 9 days ago by
qudrat.nii
▴ 10
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 5 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
3
votes
2
replies
325
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 5 days ago by
dsull
★ 5.9k • written 6 days ago by
Aaliya
▴ 10
3
votes
0
replies
197
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 5 days ago by
Ram
43k • written 6 days ago by
Claire Watson
▴ 60
0
votes
2
replies
279
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 5 days ago by
Ram
43k • written 6 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
200
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
6 days ago by
HarperReed
• 0
3
votes
3
replies
292
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 5 days ago by
GenoMax
142k • written 6 days ago by
sapuizait
▴ 10
1
vote
0
replies
156
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
6 days ago by
KABILAN
▴ 70
0
votes
0
replies
174
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 5 days ago by
Ram
43k • written 6 days ago by
SineWave
• 0
0
votes
0
replies
170
views
RNA-seq: full length gene
RNA-seq
updated 5 days ago by
Ram
43k • written 6 days ago by
Nargis
• 0
1
vote
7
replies
473
views
gvcf joint calling
WES
GATK
VCF
gVCF
4 days ago by
zihanss
• 0
0
votes
0
replies
153
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
6 days ago by
turcoa1
• 0
3
votes
3
replies
297
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 6 days ago by
swbarnes2
14k • written 6 days ago by
M
• 0
0
votes
0
replies
163
views
Designing single-stable RNA molecules
structure
RNA
6 days ago by
Edna
• 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
1
reply
219
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 6 days ago by
ATpoint
82k • written 6 days ago by
AaronJaime
• 0
0
votes
2
replies
291
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Begonia_pavonina
▴ 150
0
votes
3
replies
373
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
1 day ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
329
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
4 days ago by
Francesco
▴ 10
1
vote
7
replies
482
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 2 days ago by
bk11
★ 2.4k • written 6 days ago by
starswillfade
▴ 10
0
votes
0
replies
164
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
157
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
6 days ago by
Emily
▴ 10
1
vote
0
replies
170
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
0
replies
154
views
how to read graph_test output of monocle 3
monocle3
6 days ago by
synat.keam
▴ 100
1
vote
0
replies
202
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
6 days ago by
Assaf
▴ 10
0
votes
1
reply
490
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 6 days ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
3
votes
4
replies
344
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
6 days ago by
QX
• 0
2
votes
1
reply
236
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 7 days ago by
Adrian Altenhoff
★ 1.1k • written 7 days ago by
hemantcnaik
• 0
0
votes
0
replies
151
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
7 days ago by
Aspire
▴ 330
2
votes
5
replies
345
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
3 days ago by
analyst
▴ 30
0
votes
3
replies
296
views
Highest variable features in single cell data
single-cell
updated 5 days ago by
bk11
★ 2.4k • written 7 days ago by
Kazo
▴ 10
0
votes
1
reply
218
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 7 days ago by
Scooter
▴ 280 • written 8 days ago by
Akash D
▴ 40
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 7 days ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
1
vote
3
replies
366
views
PCA plot
DESeq2
PCAplot
updated 3 days ago by
LauferVA
4.2k • written 7 days ago by
Aaliya
▴ 10
4
votes
4
replies
432
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 4 days ago by
BioinfGuru
★ 1.7k • written 7 days ago by
Ming Tommy Tang
★ 3.9k
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 7 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
116,713 results • Page
3 of 2335
Recent Votes
Comment: Bacterial plasmid analysis
Unsupervised clustering on gene expression data
Answer: Bacterial plasmid analysis
Answer: Bacterial plasmid analysis
Define enhancer regions
A: how can i download human ribosomal reference ?
Answer: Bacterial plasmid analysis
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Recent Replies
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
ATpoint
82k
One cannot help you with this. The error is from R, yet you show not a single line of R code.
Comment: Bacterial plasmid analysis
by
Daria
▴ 10
I am the colleague! My tool groups together plasmids based on two genetic distances: containment (how much of the smaller plasmid's sequenc…
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…
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