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117,161 results • Page
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Is there any minimum number of counts in scRNAseq to consider that a gene is expressed?
scRNAseq
single-cell
seurat
scanpy
UMI
updated just now by
ATpoint
82k • written 12 minutes ago by
ev97
▴ 20
1
vote
2
replies
104
views
Error with pheatmap - 'from' must be a finite number
pheatmap
r
deseq2
updated 20 minutes ago by
zx8754
11k • written 10 hours ago by
vmpsb
• 0
0
votes
0
replies
12
views
Regarding ENSEMBL/Gencode and UCSC differences (ATAC-seq, ChiPseeker peaks annotation)
ATAC-seq
CHiPseeker
Annotation
20 minutes ago by
Manko47
• 0
2
votes
7
replies
345
views
Z score
Z-score
updated just now by
ATpoint
82k • written 5 days ago by
Akash D
▴ 60
0
votes
1
reply
41
views
Polygenic Risk Score calculation
snp
polygene
prs
variants
updated 30 minutes ago by
zx8754
11k • written 2 hours ago by
ashaneev07
▴ 20
0
votes
2
replies
292
views
Annotating single cell data automatically
single-cell
updated 2 hours ago by
Nat.Nataren
▴ 10 • written 5 weeks ago by
Gerard
• 0
0
votes
0
replies
27
views
EXOME DEPTH - CNV
CNV
3 hours ago by
Neha
• 0
801
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
0
votes
1
reply
29
views
coding and non-coding region of the viral genome
region
non-coding
coding
viral
genome
updated 20 minutes ago by
dthorbur
★ 2.0k • written 3 hours ago by
Ghada
• 0
0
votes
2
replies
60
views
dbNSFP4.7a database format to Annovar Format?
annotation
snp
dbNSFP
NGS
annovar
updated 2 hours ago by
Pierre Lindenbaum
162k • written 3 hours ago by
Clark_BioMorgan
▴ 50
0
votes
1
reply
79
views
Salmon ~ Effective Length
Salmon
updated 6 hours ago by
Rob
6.6k • written 7 hours ago by
chrisk
• 0
2
votes
2
replies
166
views
Search within posts based on tags using the Biostars API
api
meta
3 hours ago by
Bálint
▴ 10
0
votes
0
replies
44
views
Funcotator gnomAD incoherent number of output fields
gatk
fields
gnomAD
Funcotator
7 hours ago by
jaime alvarez
▴ 30
0
votes
1
reply
101
views
Help with proteomics downstream analysis
mass-spectrometry
proteomics
updated 7 hours ago by
Ram
44k • written 17 hours ago by
Álvaro
• 0
0
votes
0
replies
46
views
How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Package?
multi-omics
CNV
R
updated 7 hours ago by
Ram
44k • written 9 hours ago by
Ngrin
• 0
0
votes
0
replies
46
views
Calculating F_IS, F_IT on ancient DNA
adna
11 hours ago by
devenvyas
▴ 740
0
votes
0
replies
49
views
The number of region with the motif sequence is different between HOMER outputs
findMotifsGenome
HOMER
annotatePeaks
11 hours ago by
Aki
▴ 20
3
votes
3
replies
830
views
Cut&Run and heatmap
and
bowtie2
MACS2
updated 13 hours ago by
sogand
• 0 • written 13 months ago by
qudrat.nii
▴ 10
3
votes
10
replies
5.3k
views
6 follow
txt file to bigwig
MEME
bigwig
updated 12 hours ago by
ATpoint
82k • written 8.6 years ago by
tanni93
▴ 50
2
votes
2
replies
175
views
Help me with Heatmap
RNA-seq
R
DESeq2
updated 20 minutes ago by
zx8754
11k • written 19 hours ago by
vmpsb
• 0
0
votes
2
replies
112
views
identify the coordinate for coding and non_coding region.
coding
non_coding
16 hours ago by
Ghada
• 0
64
votes
25
replies
57k
views
22 follow
Download All The Bacterial Genomes From Ncbi
ncbi
updated 16 hours ago by
GenoMax
142k • written 11.4 years ago by
rehma.ar
▴ 290
3
votes
2
replies
134
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse
r
updated 20 minutes ago by
zx8754
11k • written 20 hours ago by
Assa Yeroslaviz
★ 1.9k
1
vote
2
replies
140
views
Salmon vs Kallisto vs RSEM
RSEM
quantification
kallisto
Salmon
2 hours ago by
Mohamed Abderrahmane
▴ 20
0
votes
0
replies
95
views
virus genome annotation
annotation
gff3
consensus
NCBI
coding_regions
16 hours ago by
Ghada
• 0
2
votes
6
replies
2.3k
views
Tool:
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart
annotation
Ensembl
updated 18 hours ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
Shred
★ 1.4k
0
votes
0
replies
87
views
Subset of Transcripts- How do I proceed with it?
Stringite
Quantification
23 hours ago by
Varsha
• 0
1
vote
2
replies
3.8k
views
How can run cd-hit-est with a clstr threshold less than 0.8?
cd-hit
cluster
updated 1 day ago by
Asaf
10k • written 6.3 years ago by
m.koohi.m
▴ 120
0
votes
2
replies
234
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
updated 1 day ago by
a.alnawfal.1992
▴ 260 • written 4 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
73
views
PyRMD
Virtual
Screening
learning
cheminformatics
machine
1 day ago by
s
• 0
3
votes
4
replies
213
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
1 day ago by
MboiTui
▴ 20
0
votes
0
replies
90
views
Determining rs ids from SNP HGV base ID?
rsID
HGV
SNP
updated 7 hours ago by
Ram
44k • written 1 day ago by
Katherine
• 0
0
votes
3
replies
262
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
updated 20 hours ago by
ATpoint
82k • written 2 days ago by
Sara
▴ 30
0
votes
1
reply
169
views
Facing problem with single cell rna seq annotation using singleR
annotation
singleR
scRNAseq
updated 1 day ago by
jared.andrews07
★ 17k • written 1 day ago by
sc_analysis
• 0
0
votes
0
replies
81
views
Imputed data doesn't match directly genotyped APOE genotype
APOE
directgenotyping
imputation
1 day ago by
kl
▴ 10
0
votes
0
replies
96
views
Tubemap multiseq
vg
1 day ago by
karciharun42
• 0
5
votes
3
replies
5.9k
views
Attempt to set 'rownames' on an object with no dimensions
R
microbiome
spieceasi
updated 1 day ago by
GenoMax
142k • written 3.6 years ago by
ks.sholohova
▴ 30
0
votes
0
replies
109
views
News:
Online course: Population Genomic Inference from Low-Coverage Whole-Genome Sequencing Data
Genotype-Likelihoods
Low-Coverage
Population-Genomics
ANGSD
updated 7 hours ago by
Ram
44k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
185
views
How to decrease the motif score?
scores
Motif
updated 10 minutes ago by
dthorbur
★ 2.0k • written 2 days ago by
Hadia
• 0
0
votes
0
replies
133
views
immuCell Abundance infiltrate
ImmuCell
Abundance
infiltrate
updated 2 days ago by
Pierre Lindenbaum
162k • written 2 days ago by
elbakri.fatimazahrae
• 0
1
vote
2
replies
234
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 1 day ago by
LauferVA
4.2k • written 3 days ago by
carolofharvest
▴ 40
0
votes
0
replies
131
views
MaxEntScan for rMATS results
MaxEntScan
rMATS
2 days ago by
adi.gershon1
• 0
0
votes
0
replies
411
views
ERROR with Maker annotation: The assumed RepeatMasker installation directory /opt/home/sony/miniconda3/envs/MAKER2/share/RepeatMasker does not ap…
RepeatMasker.
MAKER.
annotation.
3 days ago by
Sony
▴ 10
0
votes
0
replies
144
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
3 days ago by
F110152169
• 0
4
votes
2
replies
243
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq
stringtie
salmon
updated 7 hours ago by
Ram
44k • written 3 days ago by
Tonya S.
▴ 10
0
votes
3
replies
376
views
Tool:
Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvages Failed Runs
NovaDemux
NovaSeq
Illumina
Demultiplexing
Barcode
3 days ago by
Brian Bushnell
20k
2
votes
11
replies
780
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
updated 1 day ago by
Ram
44k • written 10 days ago by
hannes.bongartz
• 0
0
votes
2
replies
235
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
22 hours ago by
marco.barr
▴ 130
0
votes
0
replies
154
views
Duplicates of the same gene in Orthogroup sequence files
orthofinder
3 days ago by
niconps14
• 0
3
votes
5
replies
390
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 1 day ago by
Pierre Lindenbaum
162k • written 3 days ago by
QX
• 0
117,161 results • Page
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Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
Answer: Help me with Heatmap
Answer: Trouble understanding seemingly contradicting results of GSE analysis (contradic
Comment: Error with Pheatmap ()
A: Label selected genes in volcano plot from ggplot
A: Label selected genes in volcano plot from ggplot
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
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Comment: How to decrease the motif score?
by
dthorbur
★ 2.0k
You seem to indicate you found motifs. So why do you now want to reduce the score? Do you want to narrow your search to fewer motifs to mov…
Comment: coding and non-coding region of the viral genome
by
dthorbur
★ 2.0k
Are there already annotations published for the genome? If so, I doubt there is a dedicated tool since this is a simple task of parsing the…
Answer: Error with Pheatmap ()
by
zx8754
11k
Errors and warnings are clear, we can reproduce them with this simple example Somewhere *pheatmap* is getting a minimum value excluding NA…
Comment: Polygenic Risk Score calculation
by
zx8754
11k
A single PRS number is meaningless without background data like 1000 genomes, UK Biobank, etc.
Comment: Salmon vs Kallisto vs RSEM
by
Mohamed Abderrahmane
▴ 20
Thank you so much for your response. The two links are really helpful. I appreciate it. Have a nice day!
Comment: vg autoindex seems stuck after a week of running
by
StevieP
▴ 10
Thanks for this. As a follow-up, the process did indeed complete after 8.5 days so I guess my concerns were unwarranted in the end.
Comment: Problems when trying to use ensembl-vep
by
tomas4482
▴ 400
I won't recommend using conda for installation. The environment is somehow very difficult to set up. Conda will always fail to recognize so…
Comment: Failed to download data from EBI with ascp
by
jude
• 0
I'm also facing the same error
Comment: dbNSFP4.7a database format to Annovar Format?
by
Pierre Lindenbaum
162k
> 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: dbNSFP4.7a database format to Annovar Format?
by
Pierre Lindenbaum
162k
> But instead of I figured out most of the databases, this gave me some problems. what are those problems; This is the question.
Comment: Z score
by
Akash D
▴ 60
I wonder what is the difference between a heatmap plotted with Z score (on normalized expression values) and the one plotted with simple lo…
Answer: Annotating single cell data automatically
by
Nat.Nataren
▴ 10
Perhaps you have tried this, but I used the Seurat function as.SingleCellExperiment() and this creates an object compatible with SingleR. D…
Comment: Search within posts based on tags using the Biostars API
by
Bálint
▴ 10
Yep; I know about this option. However the problem here is that it will return only with the tags used and not the posts that are associate…
Answer: Salmon ~ Effective Length
by
Rob
6.6k
Salmon will compute the fragment length distribution based on the (probabilistically weighted) implied distance between the fragment ends g…
Comment: Error with Pheatmap ()
by
Ram
44k
Show us the output to ```r mat.z[1:10,1:10] any(is.infinite(mat.z)) ```
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