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17 results • Page
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0
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9
views
is it valid to perform a vst transformation to an rna-seq dataset to do correlation tests?
r
deseq2
vst
12 minutes ago by
pairedttest
▴ 10
0
votes
0
replies
19
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated just now by
ATpoint
82k • written 1 hour ago by
yura.grabovska
▴ 70
0
votes
0
replies
17
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
1 hour ago by
Lélé
• 0
0
votes
3
replies
87
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
3 hours ago by
Esraa
• 0
0
votes
1
reply
79
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
updated 2 hours ago by
ATpoint
82k • written 4 hours ago by
egascon
• 0
0
votes
0
replies
45
views
ReactomeGSA
ReactomeGSA
6 hours ago by
Shaimaa Gamal
▴ 10
0
votes
1
reply
71
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 2 hours ago by
GenoMax
142k • written 8 hours ago by
chrisk
• 0
0
votes
1
reply
69
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 1 hour ago by
Joe
21k • written 10 hours ago by
iqra
• 0
0
votes
0
replies
59
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 12 hours ago by
GenoMax
142k • written 13 hours ago by
Dude
• 0
0
votes
0
replies
55
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
13 hours ago by
brunofelicianodeomena
• 0
0
votes
1
reply
106
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
10 hours ago by
sansan_96
▴ 90
0
votes
1
reply
133
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 19 hours ago by
GenoMax
142k • written 20 hours ago by
bioinfo
▴ 150
0
votes
2
replies
145
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
6 hours ago by
melissa.joubert
• 0
0
votes
0
replies
87
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
22 hours ago by
ramiro.barrantes
• 0
1
vote
1
reply
121
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 20 hours ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
1
vote
4
replies
326
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 13 hours ago by
Juke34
8.6k • written 2 days ago by
Vijith
▴ 30
4
votes
7
replies
459
views
RNA seq analysis
DESeq
RNA-seq
5 hours ago by
Jacek
▴ 10
17 results • Page
1 of 1
Recent Votes
Answer: genome finishing
Answer: genome finishing
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
Answer: Add samples IDs to Seurat object when integrating different samples to do differ
A: RNA-Seq analysis with Python
Answer: Add samples IDs to Seurat object when integrating different samples to do differ
Add samples IDs to Seurat object when integrating different samples to do differential expression analysis
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Recent Replies
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Pierre Lindenbaum
161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Answer: genome finishing
by
nd48
▴ 20
What is the input? Do you have short reads (e.g. illumina 100bp paired reads)? As mentioned already, you already have the consensus i.e. c…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
biology_inform
▴ 50
I've been exploring different visualization tools like Circos and shinyCircos, and I've noticed that they require an input file similar to …
Answer: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Papyrus
★ 2.9k
If you want to plot global accessibility, maybe you would like to plot the ATAC "signal", instead of specific peaks. In a very general mann…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Pierre Lindenbaum
161k
> I haven't been able to figure out how to generate this plot. show us what you tried and the error messages
Comment: Duplicated reads (IDs) from nanopore sequencing
by
njornet
▴ 20
I think this is the answer but I can't find in the tags info about primary and secondary alignments. I've only found in the flag that the s…
Answer: Add stats to boxplot in R
by
Lélé
• 0
Hi, Have you tried switching the order of the stat_compare_means for the Wilcox with the one for kruskall-Wallis ?
Comment: genome finishing
by
Joe
21k
I may be wrong here so someone feel free to correct me, but I've never noticed a variants file from `SPAdes`, and certainly never used one …
Comment: perseus software (version 1.5.5)
by
Joe
21k
You will need to obtain the software from an official source. I believe Perseus is a paid-for program and as such sharing via the forum wou…
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
by
Joe
21k
This post does not fit the theme of this forum.
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
by
Istvan Albert
100k
this is not bioinformatics and is not a tool and as such it is off-topic on this site
Comment: calculating genomic coverage/ base overlap in R
by
Sayantani
• 0
# Install and load necessary packages if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") …
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
by
GenoMax
142k
Instead of simply posting a chunk of code it would be useful to add a line or two to say where this could would be useful. Not immediately …
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
Thanks for the link. We never use "pod5_fail" folders when re-basecalling so we did not see this issue. Current version of MinKNOW now make…
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