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Limit : this week
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181 results • Page
3 of 4
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0
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2
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65
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z-score of gene set
z-score
scRNA
gene-set
updated 32 minutes ago by
Ram
44k • written 3 hours ago by
Hien
• 0
1
vote
2
replies
222
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 8 hours ago by
colindaven
6.4k • written 1 day ago by
Dr.
• 0
1
vote
2
replies
163
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
19 hours ago by
ojaswinipandey
• 0
1
vote
1
reply
203
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 4 days ago by
Ram
44k • written 5 days ago by
dwpeng
▴ 10
1
vote
1
reply
152
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 6 days ago by
Ram
44k • written 7 days ago by
kilcdincer
▴ 10
0
votes
1
reply
137
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 6 days ago by
Ram
44k • written 7 days ago by
Emily
▴ 20
0
votes
1
reply
153
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
6 days ago by
sansan_96
▴ 90
3
votes
1
reply
335
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 6 days ago by
dariober
14k • written 7 days ago by
Holly
▴ 30
0
votes
1
reply
143
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
6 days ago by
asalimih
▴ 60
1
vote
1
reply
254
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
5 days ago by
ramiro.barrantes
• 0
0
votes
1
reply
595
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 5 days ago by
valdirbarth
▴ 20 • written 13 months ago by
Salomé
• 0
0
votes
1
reply
182
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 5 days ago by
Michael
54k • written 5 days ago by
mgranada3
▴ 30
0
votes
1
reply
182
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 5 days ago by
DGTool
▴ 20 • written 6 days ago by
iqra
• 0
0
votes
1
reply
163
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 5 days ago by
Papyrus
★ 2.9k • written 6 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
160
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 5 days ago by
GenoMax
142k • written 6 days ago by
Lélé
▴ 10
1
vote
1
reply
223
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 5 days ago by
Ram
44k • written 5 days ago by
m90
▴ 30
1
vote
1
reply
193
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 4 days ago by
Jordan M Eizenga
▴ 460 • written 15 days ago by
sarumonsus
▴ 10
0
votes
1
reply
152
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 6 days ago by
LauferVA
4.2k • written 7 days ago by
graeme.thorn
▴ 100
1
vote
1
reply
205
views
API kegg - IndexError: list index out of range
kegg
API
updated 4 days ago by
Nyksubuz
▴ 20 • written 5 days ago by
mirwa.zidi93
• 0
0
votes
1
reply
162
views
Add line under stat test
stats
R
updated 4 days ago by
Nyksubuz
▴ 20 • written 5 days ago by
Ghada
• 0
0
votes
1
reply
448
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 4 days ago by
GenoMax
142k • written 4 days ago by
huxiangyulove
• 0
0
votes
1
reply
187
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Jacek
▴ 20
1
vote
1
reply
205
views
constructing pangenome through psvcp
psvcp
pangenome
3 days ago by
analyst
▴ 50
1
vote
1
reply
344
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 2 days ago by
nguyenn6
• 0 • written 3 months ago by
star
▴ 10
2
votes
1
reply
255
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 2 days ago by
Gordon Smyth
★ 7.2k • written 3 days ago by
marineandriot
• 0
0
votes
1
reply
166
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 2 days ago by
ATpoint
82k • written 2 days ago by
rj.rezwan
• 0
0
votes
1
reply
138
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 1 day ago by
zx8754
11k • written 1 day ago by
Ali
• 0
0
votes
1
reply
128
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 1 day ago by
marco.barr
▴ 130 • written 1 day ago by
sooni
▴ 20
0
votes
1
reply
95
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 1 day ago by
GenoMax
142k • written 1 day ago by
jinyi
• 0
0
votes
1
reply
592
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 1 day ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
1
vote
1
reply
96
views
Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
niruf
• 0
0
votes
1
reply
82
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 9 hours ago by
Pierre Lindenbaum
161k • written 10 hours ago by
Peter Chung
▴ 200
1
vote
1
reply
691
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
0
votes
1
reply
108
views
vcf phasing
beagle
WhatsHap
phasing
updated 5 hours ago by
WouterDeCoster
47k • written 1 day ago by
safeassli
▴ 10
0
votes
1
reply
91
views
CreateSeuratObject taking very long
seurat
updated 4 hours ago by
Nitin Narwade
★ 1.6k • written 14 hours ago by
eae6d2e7
• 0
0
votes
1
reply
53
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 2 hours ago by
DBScan
▴ 300 • written 3 hours ago by
brunomiwa
• 0
0
votes
1
reply
31
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
vcf
identification
gene
fasta
updated 1 hour ago by
Pierre Lindenbaum
161k • written 2 hours ago by
Harshita
• 0
2
votes
1
reply
51
views
converting transcript IDs (Ensembl) to gene symbols in R
RNAseq
updated 1 hour ago by
bk11
★ 2.5k • written 2 hours ago by
ashkan
▴ 160
0
votes
1
reply
18
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 1 hour ago by
Pierre Lindenbaum
161k • written 1 hour ago by
mrk
• 0
0
votes
0
replies
136
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
Mohamed Samir
▴ 20
0
votes
0
replies
72
views
News:
Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor
Systems-Biology
Network-Analysis
R
updated 21 hours ago by
Ram
44k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
142
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 21 hours ago by
Ram
44k • written 1 day ago by
JorgeVallejo
▴ 20
0
votes
0
replies
117
views
problems in installing rDock
rDock
updated 21 hours ago by
Ram
44k • written 2 days ago by
Rodolfo Adrián
• 0
0
votes
0
replies
144
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
3 days ago by
Moinuddin
• 0
0
votes
0
replies
144
views
How can i use ESM-1v ?
VEP
ESM-1v
3 days ago by
Meto
• 0
0
votes
0
replies
157
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Long
• 0
0
votes
0
replies
148
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
3 days ago by
kilcdincer
▴ 10
0
votes
0
replies
62
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
15 hours ago by
Christopher
• 0
0
votes
0
replies
163
views
genomic region of transcription factor
search
HOMER
motif
4 days ago by
qudrat.nii
▴ 10
0
votes
0
replies
52
views
News:
Online course- Advanced Python for Life Sciences
Python
MachineLearning
Programming
DataVisualisation
10 hours ago by
carlopecoraro2
★ 2.5k
181 results • Page
3 of 4
Recent Votes
Answer: tensorQTL interaction issue
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Comment: Trimming tool
Answer: Trimming tool
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
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Recent Replies
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Shukai
• 0
Thank you Ram for the comments! Noted for future posts.
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
I am looking for diagrams, and step-by-step instructions of how to build my pipelines. I think the github is only helpful if you are a wdl…
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
oh, this is helpful. Thanks.
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Ram
44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs
by
geneontologyhelp
▴ 400
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set
by
Matthias Zepper
4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set
by
bk11
★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
by
DBScan
▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results
by
Bjorn
• 0
Thank you!
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
That's great. I will test it and let you know how it goes. Thank you.
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