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87 results • Page
2 of 2
Sort: replies
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Votes
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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
1
reply
75
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 3 hours ago by
GenoMax
142k • written 8 hours ago by
chrisk
• 0
0
votes
1
reply
80
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
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
45
views
ReactomeGSA
ReactomeGSA
6 hours ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
100
views
reference-free assembly error assessment tools
assembly
1 day ago by
lagartija
▴ 160
0
votes
0
replies
119
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
6 days ago by
asalimih
▴ 60
0
votes
0
replies
113
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 1 day ago by
Ram
43k • written 16 days ago by
atharvakarkare14
▴ 30
0
votes
0
replies
141
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
5 days ago by
singcell
• 0
0
votes
0
replies
107
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 6 days ago by
Ram
43k • written 6 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
152
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
5 days ago by
Aytaç
• 0
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
0
replies
179
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
1 day ago by
Emily
▴ 20
0
votes
0
replies
157
views
supervised admixture
supervised
admixture
5 days ago by
RT
▴ 10
0
votes
0
replies
86
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
1 day ago by
Spring
• 0
0
votes
0
replies
185
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
5 days ago by
Matvii Mykhailichenko
• 0
1
vote
0
replies
176
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
5 days ago by
eebloom
▴ 80
0
votes
0
replies
106
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
6 days ago by
Javier
• 0
0
votes
0
replies
78
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Bhavya
• 0
0
votes
0
replies
88
views
Is there a real ground truth for CNV data?
CNV
1 day ago by
jennyp0706
• 0
0
votes
0
replies
87
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
22 hours ago by
ramiro.barrantes
• 0
0
votes
0
replies
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
1
vote
0
replies
136
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
6 days ago by
Shae
▴ 10
0
votes
0
replies
55
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
13 hours ago by
brunofelicianodeomena
• 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
178
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
6 days ago by
Winter
• 0
0
votes
0
replies
116
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 6 days ago by
Ram
43k • written 6 days ago by
curious_butterfly
• 0
0
votes
0
replies
102
views
lncRNA
tcga
lncrna
2 days ago by
jain72744
▴ 10
0
votes
0
replies
105
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
3 days ago by
BioinfGuru
★ 1.7k
0
votes
0
replies
159
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 4 days ago by
Ram
43k • written 5 days ago by
naomiboldon
• 0
1
vote
0
replies
91
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
2 days ago by
tomas4482
▴ 400
0
votes
0
replies
96
views
Reference panel of normals for ensembl named refgenome
Mutect2
2 days ago by
gernophil
▴ 80
0
votes
0
replies
85
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
2 days ago by
JACKY
▴ 140
0
votes
0
replies
167
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 5 days ago by
zx8754
11k • written 5 days ago by
curious_butterfly
• 0
0
votes
0
replies
98
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
2 days ago by
atariw
▴ 10
0
votes
0
replies
153
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
5 days ago by
Samantha
• 0
87 results • Page
2 of 2
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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nd48
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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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