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105 results • Page
2 of 3
Sort: Votes
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Views
Votes
Replies
0
votes
2
replies
268
views
JASPAR2024_getMatrixSet error
getMatrixSet
JASPAR2024
updated 1 day ago by
Ram
43k • written 5 weeks ago by
maplewj
▴ 10
0
votes
2
replies
214
views
comparing VCF files
long-reads
VCF
variants
ONT
nanopore
1 day ago by
eesiribloom
▴ 50
0
votes
2
replies
286
views
PopGenome lost individual information
PopGenome
1 day ago by
Yixuan
• 0
0
votes
0
replies
97
views
Merging Hi-C datasets originating from experiments using different enzymes
enzymes
Hi-C
updated 1 day ago by
Ram
43k • written 1 day ago by
hamarillo
▴ 70
0
votes
0
replies
97
views
Convert VCF file and add covariate information
VCF
PED
PLINK
1 day ago by
asmariyaz23
▴ 10
0
votes
0
replies
95
views
bulk RNA-seq: how to remove batch effect between multiple batches and labels?
combat
batch
1 day ago by
kiraqueen
• 0
0
votes
1
reply
133
views
Cell communacations analysis. I only have the proteome of one type of cell
How
to
updated 1 day ago by
ATpoint
81k • written 1 day ago by
David Arturo
• 0
0
votes
1
reply
134
views
dbsnp flanks information
dbsnp
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
sskimvd
• 0
0
votes
0
replies
85
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
22 hours ago by
Mojtaba
• 0
0
votes
0
replies
77
views
single cell data integration approach
comparison
integration
pairwise
singlecell
20 hours ago by
Jay
• 0
0
votes
0
replies
68
views
GSEA number dimension of expression dataset
GSEA
19 hours ago by
edoardofilippi1998
• 0
0
votes
0
replies
68
views
Creating a custom ontology for peptides
ontology
peptide
18 hours ago by
Mathew
• 0
0
votes
3
replies
200
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
18 hours ago by
sarahmanderni
▴ 100
0
votes
1
reply
106
views
How can I remove duplicate SNP?
plink
updated 18 hours ago by
iraun
6.2k • written 18 hours ago by
Zhennan
• 0
0
votes
0
replies
71
views
Number of pathway result from GSVA
GSVA
18 hours ago by
Chris
▴ 260
0
votes
3
replies
208
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
updated 16 hours ago by
LChart
3.9k • written 1 day ago by
rohitsatyam102
▴ 840
0
votes
2
replies
141
views
Error with goodSamplesGenes()
R
WGCNA
16 hours ago by
bioinfo_enthusiast
• 0
0
votes
1
reply
89
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 16 hours ago by
Yogi
▴ 70 • written 17 hours ago by
Ronin
• 0
0
votes
0
replies
66
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 15 hours ago by
Ram
43k • written 17 hours ago by
r.shiasi3897
▴ 10
0
votes
1
reply
118
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 15 hours ago by
Ram
43k • written 18 hours ago by
Hajar
• 0
0
votes
2
replies
135
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
11 hours ago by
Ankit
▴ 500
0
votes
7
replies
293
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 10 hours ago by
GenoMax
140k • written 23 hours ago by
Patadu94
• 0
0
votes
0
replies
55
views
doing some ontology enrichment analysis
GO
9 hours ago by
aleksk779
• 0
0
votes
2
replies
119
views
novel and know mir156 and mir172
a
updated 9 hours ago by
gayachit
▴ 200 • written 12 hours ago by
Fadmo
• 0
0
votes
0
replies
42
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
6 hours ago by
Chris
▴ 260
0
votes
0
replies
30
views
Annotation of Complex genomes using NCBI Genome Workbench
annotation
Genome
MAKER
Workbench
4 hours ago by
SAsciences
• 0
0
votes
0
replies
30
views
In scRNA, How should I set QC standards?
scRNA
QC
3 hours ago by
mnx0723
• 0
0
votes
0
replies
11
views
Downloading a list of all refseq assembly ids, including supressed assembliey
refseq
ncbi
assembly
1 hour ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
7
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial
SPOTlight
transcriptomic
logFC
deconvolution
51 minutes ago by
M'zelle
• 0
0
votes
6
replies
329
views
STAR aligner options
STAR
21 minutes ago by
theophile
• 0
0
votes
0
replies
4
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
20 minutes ago by
liuyibin2005
• 0
0
votes
1
reply
198
views
Extract Umi sequence to readname
Sequence
FgBio
UMI
updated 6 days ago by
GenoMax
140k • written 6 days ago by
Smilesky
• 0
0
votes
0
replies
170
views
scRNA Cell Clustering Defined by Normalized Counts
Normalization
scRNA
Seurat
6 days ago by
sakura
• 0
0
votes
0
replies
177
views
Troubleshooting SCTransform Error in Seurat: "Can't use NA as row index in a tibble for assignment"
SCTransform
updated 6 days ago by
Ram
43k • written 6 days ago by
Anisha
• 0
0
votes
0
replies
173
views
Example - Meta Analysis TCGA and DepMap
Meta-Analysis
TCGA
DepMap
updated 6 days ago by
Ram
43k • written 6 days ago by
joseph.landry
▴ 50
0
votes
6
replies
406
views
Download Panther entry list
PANTHER
6 days ago by
Nicolas
• 0
0
votes
0
replies
183
views
Problem encountered during Pearson Correlation Analysis between two immune cell subtypes
scRNA-seq
biostatistics
6 days ago by
applepie
• 0
0
votes
0
replies
176
views
Questions on demultiplexing using Qiime2
demultiplexing
barcode
6 days ago by
Minh
• 0
0
votes
0
replies
164
views
How to identify the phylogenetic node age of RNAs?
phylogeny
genome
evolution
RNA-seq
5 days ago by
Apex92
▴ 280
0
votes
0
replies
155
views
Motif Scanning: HOMER vs MEME, settings?
homer
fimo
5 days ago by
mb
• 0
0
votes
0
replies
163
views
working with shapeit.
shapeit
5 days ago by
sanchit000singhdr098
• 0
0
votes
7
replies
393
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
5 days ago by
dzisis1986
▴ 70
0
votes
3
replies
297
views
How to proceed with downstream analysis after tumor-only snp calling using Varscan2?
snv
compressing
varscan
bcftools
5 days ago by
kabir.deb
▴ 80
0
votes
5
replies
403
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
5 days ago by
Learner
• 0
0
votes
0
replies
177
views
Only positive enrichment score in GSEA
enrichmentanalysis
clusterprofiler
gsea
bioconductor
rnaseq
5 days ago by
enee
▴ 10
0
votes
1
reply
225
views
PCA script correction
correction
script
PCA
updated 5 days ago by
BioinfGuru
★ 1.6k • written 5 days ago by
prity6459
• 0
0
votes
1
reply
200
views
Getting error in alignment using STAR
STAR
Error
updated 4 days ago by
Michael
54k • written 4 days ago by
pavithra.bioinformatics
• 0
0
votes
0
replies
146
views
Cromwell slurm singularity call caching
cromwell
singularity
wdl
4 days ago by
asmariyaz23
▴ 10
0
votes
0
replies
140
views
beta coefficient improves after doing mediation analysis
coefficient
mediation
beta
regression
4 days ago by
rheab1230
▴ 140
0
votes
0
replies
117
views
CIBERSORTx single cell reference sample file
scRNA-seq
CIBERSORTx
reference
4 days ago by
feather-W
• 0
105 results • Page
2 of 3
Recent Votes
Answer: vcf not indexing
Comment: Hybrid assembly Pacbio- Nanopore
Answer: vg call is time consuming
Answer: FDR and Bonferroni
Answer: FDR and Bonferroni
Answer: Choosing an FC Threshold
Answer: Choosing an FC Threshold
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Recent Replies
Comment: STAR aligner options
by
theophile
• 0
I searched the different options to increase the sensitivity. As per `--seedSearchStartLmax`, I found several answer from Alexander Dobin o…
Answer: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
liuyibin2005
• 0
Dear all I have resepctively performed linear regression analyses on two idependent datasets. One is conducted on log2 transformed CPM f…
Comment: STAR aligner options
by
theophile
• 0
Sorry, I was a bit confused by the layout, thanks for editing and clarifying!
Answer: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I want to calculate the mismatch rate on base-level, samtools stats in.bam | grep "error rate" | cut -f 2,3 error rate: 2.0…
Answer: Hybrid assembly Pacbio- Nanopore
by
colindaven
6.2k
If you have sufficient coverage of Pacbio HiFi reads - I think 30- 50X - then just use the Hifiasm https://github.com/chhylp123/hifiasm. It…
Answer: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
kayah
• 0
you should run JoinLayers() before FindAllMarkers()!!
Answer: Error occurs when migrate-n software performs "make mpis"
by
lingxue
• 0
Thank you very much. I will try to install it again according to your suggestion.
Comment: Only one read per run - Trying to use CellRangerv7
by
GenoMax
140k
https://www.ncbi.nlm.nih.gov/sra/?term=SRR16053948 Metadata indicates that this is: > Single-cell combinatorial-indexing RNA-sequencing (…
Comment: Paired layout, but one fastq file
by
GenoMax
140k
There is a BAM file available here: https://sra-pub-src-2.s3.amazonaws.com/SRR14667226/CTRL_possorted_genome_bam.bam.1 Please get that wit…
Comment: Only one read per run - Trying to use CellRangerv7
by
dsull
★ 5.6k
1. This is a comment, not an answer. Please don't post it as an answer. :) 2. This is sci-rna-seq, not 10x rna-seq. CellRanger would not …
Comment: Only one read per run - Trying to use CellRangerv7
by
Sky
▴ 10
Sorry for the delayed reply. I have included my code and the output from downloading the four files. Each dataset only resulted in one fast…
Answer: FDR and Bonferroni
by
joe
▴ 470
> Any idea why this is happening? For example, I got 1064 significant > probes from raw p-values, but only 18 from Bonferroni correction, a…
Comment: Paired layout, but one fastq file
by
Sky
▴ 10
I am also having a similar issue where there is only one fastq file but no bam file available so from my understanding I can't use bamtofas…
Comment: convert cds to seurat object
by
sooni
▴ 20
Yes, I tried with `as.Seurat`. But there is an error follwing: Error: `No data in provided assay - logcounts`. How can I solve this problem?
Comment: novel and know mir156 and mir172
by
gayachit
▴ 200
Do you have RNAseq or small RNAseq data?
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