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811 results • Page
1 of 17
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0
votes
0
replies
8
views
Integrate RDS files
integration
20 minutes ago by
Andy
▴ 50
0
votes
1
reply
46
views
What kind of statistical test does Cellranger count use?
scRNAseq
10X
Single-Cell
updated 2 hours ago by
ATpoint
72k • written 2 hours ago by
hannah
• 0
6
votes
17
replies
4.4k
views
8 follow
Eigen genes using WGCNA
wgcna
eigengenes
updated 2 hours ago by
chaco001
▴ 40 • written 4.7 years ago by
shivangi.agarwal800
▴ 120
6
votes
5
replies
96
views
Italicise annotations with pheatmap
R
Pheatmap
1 hour ago by
jamie.pike
▴ 80
1
vote
3
replies
337
views
NanoSim Error "Please specify the training reads and its reference genome!"
NanoSim
RNA-seq
LongRead
3 hours ago by
akainth
▴ 10
0
votes
1
reply
48
views
Information on sequin RNA spike in standards
Sequin
Spike-in
RNA-seq
updated 2 hours ago by
Ram
39k • written 3 hours ago by
akainth
▴ 10
0
votes
8
replies
5.7k
views
Bedtools problem : It looks as though you have less than 3 columns at line: 1. Are you sure your files are tab-delimited
bedtools
fasta
updated 4 hours ago by
Michael
• 0 • written 3.6 years ago by
Tomm
• 0
0
votes
4
replies
1.7k
views
Spatial transcriptomics without the h5 file
h5
spatial-transcriptomics
updated 3 hours ago by
Ram
39k • written 17 months ago by
jordi.diaz-manera
▴ 10
1
vote
9
replies
178
views
Trying to edit VCF file
VCF
R
bcftools
snpsaurus
updated 2 hours ago by
Ram
39k • written 4 hours ago by
peavy
• 0
0
votes
0
replies
29
views
Visualizing Graph Alignment Format via minigraph
graph
gaf
minigraph
alignment
4 hours ago by
ivazirabad
• 0
0
votes
1
reply
51
views
Get relationships and hierarchies for GO terms
GO-terms
Gene-onthology
updated 4 hours ago by
Buffo
★ 2.2k • written 5 hours ago by
DanielEB_fisk
• 0
2
votes
2
replies
176
views
Is it possible to add a dendrogram as a top annotation using ComplexHeatmap ?
Dendrogram
R
Heatmap
ComplexHeatmap
updated 6 hours ago by
jv
★ 1.2k • written 1 day ago by
Manuel
• 0
0
votes
1
reply
308
views
How to quantification proteomics data
proteomics
updated 4 hours ago by
eqoa45
• 0 • written 19 months ago by
LeeLee
▴ 10
1
vote
4
replies
134
views
Is hg38 on the multiz 30-way alignment inaccurate?
maf
UCSC
PHAST
multiz
4 hours ago by
Daniel
▴ 30
0
votes
2
replies
1.3k
views
How to perform statistical analysis of label free experiment using results from Proteome Discoverer?
Proteome-Discoverer
Label-Free
Proteomics
updated 5 hours ago by
Ram
39k • written 4.5 years ago by
k2bhide
▴ 80
0
votes
0
replies
36
views
Label free quantification in Proteome discoverer software
proteomics
quantification
spectrometry
shotgun
6 hours ago by
eqoa45
• 0
3
votes
3
replies
180
views
Perl. How to retrieve data until a keyword in GenBank?
fasta
sequence
GenBank
perl
1 hour ago by
Fungi-Beware!
▴ 10
0
votes
1
reply
93
views
CHiP-Seq Questions
DiffBind
CHiP-Seq
updated 7 hours ago by
jared.andrews07
★ 14k • written 8 hours ago by
B.N.
• 0
1
vote
0
replies
43
views
How to predict gene amplification from RNAseq and ATACseq data?
amplification
ATAC
8 hours ago by
Dan
▴ 120
0
votes
0
replies
53
views
Diff Bind Questions
DiffBind
CHiP-Seq
updated 8 hours ago by
Ram
39k • written 8 hours ago by
B.N.
• 0
3
votes
7
replies
238
views
NCBI API, Perl
API
NCBI
updated 3 hours ago by
GenoMax
129k • written 10 hours ago by
alessandro.alma00
• 0
1
vote
2
replies
98
views
hisat2 Error 137
hisat2
RNA-seq
5 hours ago by
Forough
▴ 10
0
votes
0
replies
42
views
Error occured at the PHG imputation step: allele in genotype not in the variant context
PHG
Imputation
PracticalHaplotypeGraph
Haplotype
9 hours ago by
xeod21
• 0
1
vote
0
replies
58
views
Herald:
The Biostar Herald for Monday, June 05, 2023
herald
9 hours ago by
Biostar
1.8k
2
votes
1
reply
79
views
Is RNA-Seq well suited for studying pseudogenes and lncRNA?
rna
ncRNA
transcriptome
pseudogene
rna-seq
updated 6 hours ago by
rpolicastro
12k • written 9 hours ago by
Kermit
▴ 80
1
vote
5
replies
147
views
Embryo transcriptome
database
transcriptome
SRA
updated 2 hours ago by
ATpoint
72k • written 10 hours ago by
firefox91
• 0
1
vote
3
replies
109
views
Obtain a --gene-trans-map file after rnaSPAdes
rnaSPAdes
Trinity
9 hours ago by
UserA
• 0
1
vote
0
replies
57
views
Tutorial:
Get a list of genes associated with a drug in 1 min
drug
genes
drug-targets
updated 8 hours ago by
Ram
39k • written 10 hours ago by
john
▴ 10
2
votes
3
replies
221
views
Getting species names and taxa id from assembly accession number
efetch
biopython
entrez
updated 10 hours ago by
MirianT_NCBI
▴ 590 • written 1 day ago by
kwhiggins27
▴ 10
0
votes
0
replies
44
views
How to extract only neutral markers from low-coverage whole genome sequencing?
low-coverage
whole-genome-sequencing
updated 8 hours ago by
Ram
39k • written 10 hours ago by
beausoleilmo
▴ 530
0
votes
2
replies
95
views
Installation of PPFinder
gene-prediction
PPFinder
pseudogene
updated 8 hours ago by
Ram
39k • written 11 hours ago by
subashini.fbtpb106
• 0
0
votes
4
replies
134
views
Difference between USCS exon coordinates and ensembl
exons
Ensembl
8 hours ago by
amy__
▴ 50
2
votes
3
replies
181
views
Gene enrichment analysis
Go
enrichment
r
gene
updated 12 hours ago by
GenoMax
129k • written 19 hours ago by
Eliza
• 0
0
votes
0
replies
54
views
Why sone miRNAs are not present in TCGA data
TCGA
miRNA
RNA-seq
13 hours ago by
nicolo.gualandi
• 0
0
votes
4
replies
173
views
Getting same value for start and end position, "DNA methylation"
DNAmethylation
methylkit
updated 13 hours ago by
ATpoint
72k • written 18 hours ago by
Pankaj
• 0
1
vote
4
replies
283
views
How to calculate TPM from featureCounts output
rna-seq
TPM
featurecounts
updated 8 hours ago by
Ram
39k • written 1 day ago by
survive
• 0
3
votes
10
replies
1.6k
views
6 follow
How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by cell barcode?
10xgenomics
RNAseq
scRNA
CB
updated 14 hours ago by
biofalconch
▴ 580 • written 10 months ago by
MYousry
▴ 20
0
votes
0
replies
51
views
Prediction of altrered metabolites from altered gene expression
Gene
Metabolites
14 hours ago by
english.server
▴ 290
0
votes
3
replies
137
views
CNNScoreVariants Error
CNNscore
updated 10 hours ago by
Pierre Lindenbaum
154k • written 16 hours ago by
bestone
▴ 10
1
vote
1
reply
96
views
Finding Enhancers using Genomation library
Genomation
updated 16 hours ago by
ATpoint
72k • written 18 hours ago by
Pankaj
• 0
0
votes
5
replies
395
views
convert data frame with character column to data frame with integer column
r
updated 17 hours ago by
Basti
★ 1.6k • written 3 days ago by
atemedorri137798
• 0
0
votes
0
replies
124
views
Pore-C-Snakemake output files
contacts
updated 18 hours ago by
zhang yi xing
▴ 10 • written 5 days ago by
oksana03fel
• 0
3
votes
3
replies
281
views
Why is coordinate sort required before findng read depths?
wgs
sambamba
updated 19 hours ago by
zhang yi xing
▴ 10 • written 3 days ago by
guntul
• 0
2
votes
2
replies
132
views
how to sort unique seq from fasta files
fasta
updated 19 hours ago by
shenwei356
8.1k • written 20 hours ago by
Sapphire
• 0
2
votes
2
replies
169
views
I need help with a blast command, please help
linux
blast
updated 8 hours ago by
Ram
39k • written 1 day ago by
neto.pvp
• 0
1
vote
1
reply
138
views
Is there a way to add a transcript to EnsDb.Hsapiens.v86?
ensembldb
GenomicFeatures
R
Bioconducter
EnsDb.Hsapiens.v86
20 hours ago by
Daniel
▴ 30
2
votes
2
replies
136
views
How to make the profile line of `deepTools::plotHeatmap` more smooth?
plotHeatmap
deepTools
1 day ago by
Dan
▴ 120
0
votes
3
replies
193
views
Convert Bam file to Fastq
Fastq
Bam
updated 8 hours ago by
Ram
39k • written 1 day ago by
وفاء
• 0
0
votes
0
replies
104
views
Job:
Data Engineer / Bioinformatician- AZ-Crick-Imperial College: Molecular Glue Discovery Partnership
data-engineering
drug-discovery
data-science
updated 8 hours ago by
Ram
39k • written 1 day ago by
Sergio Martínez Cuesta
▴ 220
0
votes
4
replies
172
views
variant allelic fraction
vep
1 hour ago by
malm
• 0
811 results • Page
1 of 17
Recent Votes
Comment: Italicise annotations with pheatmap
Answer: integrate single cell RNA sequencing data
Answer: integrate single cell RNA sequencing data
Comment: Perl. How to retrieve data until a keyword in GenBank?
Answer: Perl. How to retrieve data until a keyword in GenBank?
Comment: Italicise annotations with pheatmap
Answer: Italicise annotations with pheatmap
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Recent Replies
Comment: Perl. How to retrieve data until a keyword in GenBank?
by
Fungi-Beware!
▴ 10
THANK YOU!! Your method works!! And by removing: $data = ''; I figured out how to retrieve the annotation info with a prompt: …
Comment: variant allelic fraction
by
malm
• 0
Ok but i have only vep files i don't have vcf files
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
Yeeshouw
• 0
Yes, I am inputting a GTF file. I reviewed the `[featureCounts][1]` documentation, and I could not find this `extraAttributes` parameter. …
Comment: Italicise annotations with pheatmap
by
jamie.pike
▴ 80
@ATpoint Very true! I'm not so familiar with many image editing software and I wonder if it will be just as quick for me to try in R, but I…
Comment: Italicise annotations with pheatmap
by
jamie.pike
▴ 80
You're right, I was trying to save time and not write for in ComplexHeatmap, but using @Trivas ComplexHeatmap::pheatmap() should help! Than…
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
Yeeshouw
• 0
Thank you very much for information! I am able to see this column you mention.
Comment: Italicise annotations with pheatmap
by
ATpoint
72k
I might be the party pooper but I generally think that these sorts of aesthetics should be done later in something like Inkscape. In R do t…
Comment: Embryo transcriptome
by
ATpoint
72k
Just one, that is how the convention is. One sample (SRX...) can have one or many SRR entries. If many you can merge them prior to quantifi…
Comment: What kind of statistical test does Cellranger count use?
by
ATpoint
72k
Clustering is not a statistical test with p-values. It is unclear what you mean. Actually, I would just ignore everything that the blackbox…
Comment: Information on sequin RNA spike in standards
by
Ram
39k
I'd try emailing the authors for a link.
Comment: Calculate Radius of Gyration [python 3]
by
Franco
• 0
I know it's been a long time since this been discussed. Anyways, I did a script of mine to calculate the gyration radius for a couple of PD…
Answer: Eigen genes using WGCNA
by
chaco001
▴ 40
I think this is very old, but I think the commenters are misinterpreting your (miswritten) question. Based on the back-and-forth, you aren'…
Comment: Embryo transcriptome
by
firefox91
• 0
Thank you so much ! I find the articles but not the data of the papers, do you have a link please ?
Comment: Perl. How to retrieve data until a keyword in GenBank?
by
Pierre Lindenbaum
154k
cross posted: https://stackoverflow.com/questions/76405846
Comment: Embryo transcriptome
by
firefox91
• 0
This result from SRA for example. I can download the file with the SRA toolkit but how to know how many transcriptomes this file co![enter …
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