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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
34
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
25 minutes ago by
Shukai
• 0
0
votes
0
replies
23
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 1 hour ago by
GenoMax
142k • written 2 hours ago by
LuciaNhu
• 0
0
votes
1
reply
32
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 2 hours ago by
Pierre Lindenbaum
161k • written 2 hours ago by
Harshita
• 0
2
votes
0
replies
31
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
Bioinformatics
csaw
2 hours ago by
Rafael Soler
★ 1.2k
0
votes
0
replies
35
views
How does Kraken2 deal with poor read qualities?
kraken
qiime2
kraken2
qiime
updated 1 hour ago by
GenoMax
142k • written 3 hours ago by
Christopher
• 0
0
votes
1
reply
56
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 3 hours ago by
DBScan
▴ 300 • written 3 hours ago by
brunomiwa
• 0
0
votes
0
replies
38
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
4 hours ago by
Ayda Ecem
• 0
0
votes
3
replies
88
views
Generating a Bed file from a Fasta file
bedfile
Sequences
Random
NullSeq
updated 3 hours ago by
Pierre Lindenbaum
161k • written 4 hours ago by
pirku
• 0
0
votes
0
replies
49
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
7 hours ago by
Yao
▴ 30
0
votes
0
replies
54
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
9 hours ago by
dawnyipingzou
• 0
0
votes
4
replies
115
views
Where to find old version of GATK best practice
gatk
26 minutes ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
83
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
0
votes
1
reply
93
views
CreateSeuratObject taking very long
seurat
updated 4 hours ago by
Nitin Narwade
★ 1.6k • written 14 hours ago by
eae6d2e7
• 0
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
2
replies
146
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
3 hours ago by
Bjorn
• 0
0
votes
3
replies
213
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 20 hours ago by
marco.barr
▴ 130 • written 1 day ago by
Mohamed Samir
▴ 20
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
0
replies
81
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 1 day ago by
Ram
44k • written 1 day ago by
ev97
▴ 20
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
0
replies
73
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA
ENCORI
curl
microRNA
starBase
1 day ago by
V_Vibes
• 0
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
94
views
transcriptome annotation
annotation
trinity
transcriptome
updated 1 day ago by
Ram
44k • written 1 day ago by
Asim Bin Arshad
• 0
0
votes
5
replies
220
views
Why most genes have high padj values
RNA-seq
DEG
updated 1 day ago by
Ram
44k • written 1 day ago by
mnx0723
• 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
4
replies
243
views
GO analysis: p-value range
GO
R
updated 1 day ago by
Matthias Zepper
4.6k • written 1 day ago by
sooni
▴ 20
0
votes
0
replies
100
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
1 day ago by
Maryam
• 0
1
vote
8
replies
445
views
Add stats to the plot
R
updated 10 hours ago by
marco.barr
▴ 130 • written 2 days ago by
Ghada
• 0
0
votes
4
replies
328
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
1 day ago by
Bibi
• 0
0
votes
0
replies
111
views
handling bio replicates for chromHMM
replicates
chromHMM
2 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
102
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
2 days ago by
DGTool
▴ 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
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
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
144
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
3 days ago by
Moinuddin
• 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
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
163
views
genomic region of transcription factor
search
HOMER
motif
4 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
379
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 3 days ago by
dthorbur
★ 2.0k • written 4 days ago by
BATMAN
• 0
0
votes
6
replies
370
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
3 days ago by
hannes.bongartz
• 0
0
votes
0
replies
150
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 4 days ago by
GenoMax
142k • written 4 days ago by
yura.grabovska
▴ 90
1
vote
1
reply
205
views
constructing pangenome through psvcp
psvcp
pangenome
3 days ago by
analyst
▴ 50
1
vote
6
replies
353
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
6 hours ago by
Umer
▴ 50
0
votes
2
replies
257
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
melissachua90
▴ 70
0
votes
0
replies
136
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
4 days ago by
Varsha
• 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
0
replies
153
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
4 days ago by
O.rka
▴ 720
0
votes
4
replies
353
views
Merge clusters in Seurat UMAP
seurat
umap
4 days ago by
kilcdincer
▴ 10
1,000 results • Page
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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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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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