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49 results • Page
1 of 1
Sort: Votes
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Views
Votes
Replies
8
votes
8
replies
570
views
How to filter .fasta file based on conditional statement
abundance
filtering
fasta
vsearch
updated 11 hours ago by
Brian Bushnell
19k • written 8 days ago by
rob_DNA
▴ 20
8
votes
7
replies
462
views
p-value combination methods
rnaseq
NB-GLM
p-value
meta-Analysis
updated 13 hours ago by
Istvan Albert
99k • written 2 days ago by
sehriban.buyukkilic
• 0
4
votes
5
replies
831
views
Extracting only soft/hard clipped reads from a bam file
bam
reads
NGS
clipped
data_analysis
updated 13 hours ago by
Pierre Lindenbaum
158k • written 14 months ago by
jcn
▴ 30
4
votes
5
replies
1.9k
views
How to do simple pathway analysis?
rna-seq
genome
gene
updated 3 hours ago by
AK
★ 2.2k • written 4.5 years ago by
Seq225
▴ 110
3
votes
4
replies
230
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 32 minutes ago by
GenoMax
136k • written 1 day ago by
newbee
▴ 40
3
votes
4
replies
203
views
Is there a need to batch correct FPKM or TPM values for within sample comparison
Batch
correction
3 hours ago by
CTLong
▴ 20
3
votes
2
replies
272
views
BBtools bug in reporting the number of substitutions in the console output, it seems to report insanely high rates of heterozygosity
SNP
bbtools
updated 10 hours ago by
harold.smith.tarheel
★ 4.9k • written 16 hours ago by
Axzd
▴ 50
3
votes
2
replies
243
views
Mapping quality in `vg giraffe`
vg
19 hours ago by
Wenhai
• 0
2
votes
3
replies
170
views
Is bisulfite-seq data from different studies comparable with each other?
Methylation
updated 18 hours ago by
Basti
★ 1.9k • written 22 hours ago by
CTLong
▴ 20
2
votes
5
replies
282
views
Tools or R / Python packages to perfom ML models
Python
machine-learning
R
transcriptomics
updated 12 hours ago by
Michael
53k • written 18 hours ago by
sil_bioinfo
▴ 30
2
votes
2
replies
173
views
R script in docker
R
Visual_studio_code
Docker
15 hours ago by
mrashad
▴ 70
2
votes
8
replies
614
views
6 follow
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 6 hours ago by
ATpoint
78k • written 18 days ago by
ellen.francis
▴ 10
2
votes
11
replies
660
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
14 hours ago by
sil_bioinfo
▴ 30
1
vote
2
replies
192
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
23 hours ago by
eamaunders
• 0
1
vote
1
reply
109
views
Bulk and Single Cell RNA-seq online course
single_cell_RNA-seq
bulk_RNA-seq
online_course
updated 8 hours ago by
swbarnes2
13k • written 13 hours ago by
ire
• 0
1
vote
5
replies
287
views
How can I map coordinates between two strains of yeast?
coordinates
yeast
genome
mapping
fasta
22 minutes ago by
Jimmy
▴ 10
0
votes
0
replies
55
views
Should I scale all genes in single cell Seurat?
singlecell
13 hours ago by
synat.keam
▴ 80
0
votes
3
replies
171
views
In what case there are RR reads but no LL reads when detect inversions using IGV?
IGV
inversion
updated 13 hours ago by
Istvan Albert
99k • written 17 hours ago by
Jingfang
• 0
0
votes
2
replies
247
views
Can FPKM be used to create bar graphs for DEGs?
RNA-seq
11 hours ago by
junli1988
• 0
0
votes
1
reply
113
views
Where do these snpeff annotation come from?
snpeff
updated 11 hours ago by
Istvan Albert
99k • written 15 hours ago by
curious
▴ 730
0
votes
0
replies
57
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
11 hours ago by
bioinfo
▴ 140
0
votes
3
replies
178
views
ERROR FILE EXTENSION
Prokka
23 hours ago by
syirah4
• 0
0
votes
2
replies
864
views
Ipyrad de novo for variant calling
snps
updated 10 hours ago by
Betsy
• 0 • written 2.5 years ago by
giulia.trauzzi
▴ 10
0
votes
0
replies
41
views
how to download the VCF/MAF files from cBioportal genie site
cBioportal
mutation
VCF
TMB
9 hours ago by
luckyday1661
• 0
0
votes
0
replies
50
views
GO categorization
Ontology
Gene
9 hours ago by
m.habib
• 0
0
votes
1
reply
76
views
gene set enrichment analysis- by enrichGO
rna-seq
GO
enrichment
updated 9 hours ago by
Istvan Albert
99k • written 9 hours ago by
CL
• 0
0
votes
1
reply
339
views
Loftee no splice site annotations
Loftee
VEP
updated 8 hours ago by
AMARU
• 0 • written 21 months ago by
Filago
▴ 90
0
votes
0
replies
60
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
7 hours ago by
Ty
• 0
0
votes
0
replies
50
views
How to estimate -g genome-size for Flye for de novo genome or for --meta mode when using Metaflye?
assembly
fasta
genomics
nanopore
pacbio
7 hours ago by
O.rka
▴ 710
0
votes
2
replies
137
views
Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
metabolomic
bioinformatic
updated 5 hours ago by
Kevin Blighe
86k • written 11 hours ago by
Giovana
• 0
0
votes
13
replies
867
views
Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cell Ranger.
fixed-RNA-profiling
chromium
cellranger
scFFPE
updated 4 hours ago by
MohammadAlkadi
▴ 70 • written 5 weeks ago by
bk11
★ 1.8k
0
votes
1
reply
57
views
DIAMOND tutorial
tutorial
DIAMOND
updated 2 hours ago by
GenoMax
136k • written 4 hours ago by
sooni
▴ 10
0
votes
1
reply
61
views
How to get multiple protein domain database domain name from id's
annotations
blast2go
domain
domains
proteins
updated 2 hours ago by
GenoMax
136k • written 9 hours ago by
Nicolas
• 0
0
votes
0
replies
52
views
Annotate Unplaced Scaffold with Chromosome Information
assembly
annotation
scaffold
Chromosome
11 hours ago by
Trevor
• 0
0
votes
0
replies
62
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE
admixture
22 hours ago by
maxlaubstein
• 0
0
votes
0
replies
70
views
how to calculate intramodular connectivity
WGCNA
intramodularConnectivity
21 hours ago by
hellokwmin
• 0
0
votes
3
replies
153
views
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics
nucleotide_diversity
vcf
21 hours ago by
J
• 0
0
votes
1
reply
133
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
updated 19 hours ago by
Nitin Narwade
★ 1.5k • written 1 day ago by
tss243
• 0
0
votes
4
replies
196
views
Can you help me to download list of miRNA from a SRA under a bioproject ?
bioproject
mirna
updated 19 hours ago by
Nitin Narwade
★ 1.5k • written 20 hours ago by
abourrieau
• 0
0
votes
2
replies
200
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 19 hours ago by
fracarb8
★ 1.3k • written 1 day ago by
synat.keam
▴ 80
0
votes
1
reply
104
views
Salmon indices differences
salmon
RNAseq
index
refgenie
decoy
updated 18 hours ago by
ATpoint
78k • written 19 hours ago by
enee
▴ 10
0
votes
9
replies
426
views
Where is the index command?
samtools
updated 18 hours ago by
Michael
53k • written 1 day ago by
luque007
• 0
0
votes
0
replies
120
views
Job:
Bioinformatican/Data Scientist, Transplant Immunology/Genetics, Medical University of Vienna, Austria
RiskPrediction
NGS
SNP
ExomeSequencing
GeneticRiskScore
16 hours ago by
aheinzel
▴ 130
0
votes
5
replies
303
views
HTseq reports missing attribute name
htseq
updated 16 hours ago by
Istvan Albert
99k • written 3 days ago by
Bjorn
• 0
0
votes
1
reply
157
views
String App in Cytoscape
App
String
cytoscape
updated 15 hours ago by
Scooter
▴ 180 • written 3 days ago by
hellokwmin
• 0
0
votes
1
reply
238
views
Gene Ontology enrichment with BINGO and ClueGO
BINGO
Cytoscape
ClueGO
Gene
Ontology
updated 15 hours ago by
Scooter
▴ 180 • written 13 days ago by
David R
▴ 20
0
votes
1
reply
199
views
How I add new organism "Beauveria bassiana (strain ARSEF 2860)" in ClueGo plug-in of cytoscape?
cytoscape
updated 15 hours ago by
Scooter
▴ 180 • written 25 days ago by
A
• 0
0
votes
1
reply
114
views
PAML Troubleshooting Help
PAML
codeml
updated 15 hours ago by
dthorbur
▴ 880 • written 20 hours ago by
sebabiokr
▴ 10
0
votes
1
reply
70
views
News:
Course: Genome Assembly and Annotation
GenomeAssembly
GenomeAnnotation
Longreads
Bioinformatics
Biodiversity
updated 14 hours ago by
sil_bioinfo
▴ 30 • written 15 hours ago by
carlopecoraro2
★ 2.4k
49 results • Page
1 of 1
Recent Votes
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
Seurat integration of two datasets - GSE126783
about batch correction in scRNA-seq
How to compare two Seurat object (sample) in order to find top markers?
How do I resolve an integration error in Seurat?
The difference between merge and integration with Seurat objects
Analyzing single cell RNA seq with multiple samples and conditions
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Recent Replies
Comment: How can I map coordinates between two strains of yeast?
by
Jimmy
▴ 10
Yes (S. cerevisiae)
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
GenoMax
136k
> less than 100 for some samples Hmm. That is surprising but then in light of that fact ~20% recovery of cells does not sound bad.
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
newbee
▴ 40
Thanks for raising these valid points. I do not have the answer right now. Lately, I heard from the PI that they started with a small numbe…
Comment: How to get multiple protein domain database domain name from id's
by
GenoMax
136k
A list of InterPro domains is available: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list
Answer: DIAMOND tutorial
by
GenoMax
136k
`DIAMOND` has a wiki page: https://github.com/bbuchfink/diamond/wiki Links for DIAMOND papers are here: https://github.com/bbuchfink/diamo…
Comment: How to do simple pathway analysis?
by
AK
★ 2.2k
Hi [he1k](https://www.biostars.org/u/139817/), Please use the following script which downloads and parses the keg data on the fly: [keg_hi…
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
CTLong
▴ 20
That's what I would assume, because we are not taking into account cross sample differences here. Thanks
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
CTLong
▴ 20
That's a good point. So its probably safest to not batch correct for within sample comparisons I guess?
Answer: Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cel
by
MohammadAlkadi
▴ 70
What is the purpose of doing so? I tried to do that by using the bam file generated by CellRanger. One **important detail** if you are work…
Comment: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
by
Kevin Blighe
86k
Thank you - appreciate the translation.
Answer: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
by
Kevin Blighe
86k
Em geral, uma taxa de descoberta falsa de 5% (p ajustado<0,05 ) deve ser usada para qualquer teste estatístico em que múltiplas hipóteses i…
Answer: WGCNA tutorial docs needed: Horvath Lab site down
by
ATpoint
78k
See link here from the developer: https://bioinformatics.stackexchange.com/a/21886/16676
Comment: WGCNA tutorial docs needed: Horvath Lab site down
by
Katie
• 0
I would also appreciate the PDFs if anyone has them please
Answer: Loftee no splice site annotations
by
AMARU
• 0
Hey, did you solve it? I am having a very similar issue. Thanks
Answer: Bulk and Single Cell RNA-seq online course
by
swbarnes2
13k
I'd start by getting tutorials for R libraries like DESeq, EdgeR, Seurat, etc, and learn by doing.
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