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186 results • Page
2 of 4
Sort: Votes
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Views
Votes
Replies
1
vote
2
replies
1.6k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 3 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
1
vote
1
reply
137
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 3 days ago by
andres.firrincieli
3.6k • written 3 days ago by
kacollier
▴ 30
1
vote
0
replies
147
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
5 days ago by
Biostar
2.7k
1
vote
11
replies
5.5k
views
Truncated Bam Error
R
next-gen
sequencing
software error
updated 6 days ago by
guanghao
• 0 • written 6.1 years ago by
vivekruhela
▴ 20
1
vote
3
replies
298
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
6 days ago by
Dora
▴ 10
1
vote
0
replies
128
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
2 days ago by
Shae
▴ 10
1
vote
10
replies
867
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 6 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
1
vote
2
replies
175
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
4 days ago by
robert.flynn.21
• 0
1
vote
4
replies
365
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
4 days ago by
heelpPlease
• 0
1
vote
1
reply
434
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 2 days ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
1
vote
1
reply
206
views
Gene ontology and homologs
gene-ontology
updated 5 days ago by
geneontologyhelp
▴ 400 • written 6 days ago by
beshka194
• 0
1
vote
2
replies
214
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 2 days ago by
Michael
54k • written 3 days ago by
ashaneev07
▴ 20
1
vote
6
replies
694
views
anRichment is missing
WGCNA
anRichment
updated 5 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
1
vote
7
replies
495
views
Question regarding WGCNA
WGCNA
Network-construction
2 days ago by
deepak
• 0
1
vote
0
replies
174
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
2 days ago by
eebloom
▴ 80
1
vote
2
replies
233
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 5 days ago by
zx8754
11k • written 5 days ago by
snajafy
• 0
1
vote
5
replies
413
views
HCL database download
HCL
updated 4 days ago by
Ram
43k • written 8 days ago by
sooni
▴ 20
1
vote
3
replies
228
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 2 days ago by
GenoMax
142k • written 3 days ago by
cput
• 0
1
vote
2
replies
316
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
5 days ago by
M.
▴ 30
1
vote
5
replies
337
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 3 days ago by
Michael
54k • written 5 days ago by
qwertyuiop26
• 0
1
vote
0
replies
152
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 6 days ago by
zx8754
11k • written 8 days ago by
Emilie
▴ 10
1
vote
2
replies
184
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
3 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
0
replies
127
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 5 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
sarumonsus
▴ 10
1
vote
7
replies
514
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 1 day ago by
Pierre Lindenbaum
161k • written 4 days ago by
schmince
• 0
1
vote
9
replies
346
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 1 day ago by
i.sudbery
19k • written 4 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
4
replies
390
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 1 day ago by
GenoMax
142k • written 24 days ago by
aniigodwinn
• 0
1
vote
4
replies
291
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
1 day ago by
rackbersingh
• 0
1
vote
3
replies
301
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
6 days ago by
Lada
▴ 30
1
vote
2
replies
247
views
Downloading full alignments from Pfam
pfam
6 days ago by
bef1
• 0
1
vote
3
replies
202
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 1 day ago by
Ram
43k • written 1 day ago by
Omics data mining
▴ 260
1
vote
3
replies
175
views
Tassel 5 GBS: Is there something wrong with my fastqs?
tassel
fastq
gbs
updated 1 day ago by
GenoMax
142k • written 1 day ago by
meck
• 0
1
vote
2
replies
176
views
Genome Assembly task + Protein Translation, assignment advice on a question
sequence-analysis
protein-synthesis
22 hours ago by
rackbersingh
• 0
1
vote
2
replies
257
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 4 days ago by
Weiwen
• 0 • written 5 days ago by
MICOS
▴ 10
1
vote
5
replies
322
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 5 days ago by
Ram
43k • written 6 days ago by
snajafy
• 0
1
vote
1
reply
261
views
Seurat V5 integration
Seurat
integration
updated 3 days ago by
Ram
43k • written 6 days ago by
starswillfade
▴ 10
0
votes
0
replies
99
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
1 day ago by
beantkapoor16
• 0
0
votes
2
replies
257
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 1 day ago by
GenoMax
142k • written 8 days ago by
Ximena
• 0
0
votes
1
reply
163
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 1 day ago by
curious
▴ 750 • written 1 day ago by
SeoGyun
• 0
0
votes
2
replies
195
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 1 day ago by
Ram
43k • written 2 days ago by
sainavyav22
• 0
0
votes
1
reply
133
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 1 day ago by
Ram
43k • written 1 day ago by
Shwetha
• 0
0
votes
0
replies
102
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 1 day ago by
Ram
43k • written 1 day ago by
naomiboldon
• 0
0
votes
0
replies
111
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
updated 1 day ago by
GenoMax
142k • written 10 days ago by
meck
• 0
0
votes
10
replies
350
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
updated 1 day ago by
swbarnes2
14k • written 1 day ago by
Tuck898
• 0
0
votes
4
replies
263
views
Correlation Analysis
statistics
methylation
NGS
expression
1 day ago by
Researcher
▴ 30
0
votes
2
replies
212
views
How are score_weights calculated in this code?
single-cell
23 hours ago by
carolofharvest
▴ 40
0
votes
0
replies
72
views
imputation through beagle
panel
beagle
reference
imputation
22 hours ago by
analyst
▴ 50
0
votes
1
reply
109
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
updated 20 hours ago by
Pierre Lindenbaum
161k • written 23 hours ago by
analyst
▴ 50
0
votes
4
replies
233
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
13 hours ago by
ajbarrett98
• 0
0
votes
1
reply
140
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
updated 12 hours ago by
fracarb8
★ 1.6k • written 21 hours ago by
beginner123
• 0
0
votes
1
reply
144
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 11 hours ago by
Mathew
▴ 90 • written 1 day ago by
Christopher
• 0
186 results • Page
2 of 4
Recent Votes
Gff To Vcf
Comment: Longest transcript variant per gene
Comment: Longest transcript variant per gene
Answer: Longest transcript variant per gene
Answer: Longest transcript variant per gene
Comment: Longest transcript variant per gene
Comment: Longest transcript variant per gene
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Recent Replies
Answer: input file in rmats
by
Mathew
▴ 90
Hi, In the example they give in their GitHub (https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/README.md): They have 2 sample groups wi…
Comment: Longest transcript variant per gene
by
Mathew
▴ 90
I'm glad it worked well for you! Good luck with the rest of your project. I wish you the best.
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thanks so much
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Hello again, It works very well, thank you very much for this solution.
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Hello Mathew, Thanks for your answer, I'll try it and come back.
Answer: Longest transcript variant per gene
by
Mathew
▴ 90
Hi, why not write code to extract the longest variant? I copied these two in a txt file called "input.txt", and made three dummy variants …
Comment: Longest transcript variant per gene
by
GenoMax
142k
https://www.biostars.org/p/107759/<br> https://www.biostars.org/p/403649/ <!-- this is it -->
Answer: Kraken2 database
by
Mathew
▴ 90
Sorry, what analysis are you trying to perform with these databases? Based on your question, it appears you are using Kraken2 and Bracken.…
Comment: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
by
Mathew
▴ 90
I looked up a publication using CIBERSORT to see how they got the package, and indeed they acquired it through official website application…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py
by
fracarb8
★ 1.6k
If you are using R, you should check the liana R implementation (https://github.com/saezlab/liana).
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Thank you Pierre, I am going to take some time to get my head around this and report back if it works.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Thanks for the crosspost! Just trying to get things figured out.
Answer: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
by
ATpoint
82k
To the best of my knowledge, CIBERSORT is and has always and only been available via the official website application from Stanford. Whatev…
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Update of BioLabDonkey - Version 5.6 - In silico PCR function is added.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
cross posted: https://stackoverflow.com/questions/78462732/ > Please mind that posting the same question to multiple sites can be perceive…
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