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81 results • Page
2 of 2
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Views
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129
views
Advice on telling if two SNPs are on the same haplotype
ldpair
halplotype
co-occurance
gnomad
snp
1 day ago by
amy__
▴ 160
0
votes
0
replies
129
views
computeGCBias outputs
GC
bam
deepTools
GCbias
4 days ago by
pablo
▴ 300
1
vote
0
replies
126
views
How should I regenotype VCFs using vg?
vg
2 days ago by
Ricky
▴ 10
1
vote
1
reply
123
views
Seeking Help with Cell Ranger Multi Error in fixed-RNA-profiling
chromium
fixed-RNA-profiling
cellranger
updated 4 days ago by
Ram
43k • written 4 days ago by
lam
• 0
0
votes
1
reply
123
views
Calculating (Groupwise) Log2fold change using values obtained from SST-RMA?
SST-RMA
genes
TAC
thermofisher
foldchange
updated 5 days ago by
ATpoint
81k • written 5 days ago by
purple909
• 0
0
votes
1
reply
122
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
updated 16 hours ago by
Ram
43k • written 22 hours ago by
Learner
• 0
0
votes
0
replies
122
views
stat test
stattest
chi2
updated 2 days ago by
GenoMax
140k • written 2 days ago by
NLL
• 0
0
votes
0
replies
121
views
Analyzing differentially methylated regions from Nanopore long read data?
bioinformatics
Long
read
sequencing
methylation
2 days ago by
Arton
• 0
0
votes
0
replies
119
views
HADDOCK 2.4
Protein
Docking
6 days ago by
Preeti
• 0
0
votes
0
replies
118
views
Music2 human to mouse deconvolution
deconvolution
liftover
music2
4 days ago by
rbronste
▴ 420
0
votes
0
replies
115
views
How to generate a comparative map using CGview?
genome
map
CGView
1 day ago by
marongiu.luigi
▴ 710
0
votes
1
reply
110
views
Bed file
bedfile
updated 4 days ago by
Pierre Lindenbaum
160k • written 4 days ago by
Jeet
• 0
0
votes
0
replies
108
views
comparing sc-seq combination and bulk-sequencing
bulk-sequencing
sc-sequencing
1 day ago by
润达
• 0
0
votes
1
reply
107
views
Haddock 2.4
Protein
Docking
updated 21 hours ago by
dthorbur
★ 1.6k • written 22 hours ago by
Preeti
• 0
0
votes
0
replies
107
views
Pindel zygosity determination
depth
vaf
pindel
Zygosity
4 days ago by
arya.sagittarius
▴ 10
0
votes
0
replies
99
views
What to do with multiple genes in ballgown?
STAR
ballgown
DESeq2
5 days ago by
markusz
▴ 10
0
votes
0
replies
96
views
Issue to run gatk4 spark
gatk
spark
5 days ago by
Mojtaba
• 0
0
votes
0
replies
95
views
ImmuCellAI
RStudio
ImmuCellAI
updated 5 days ago by
Ram
43k • written 5 days ago by
sana
• 0
0
votes
0
replies
92
views
Polysome profiling data
Polysome
updated 4 days ago by
Ram
43k • written 5 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
83
views
Difference between reading concatenated PE reads into jellyfish and merging paired end .jf outputs independently
Jellyfish
Kmer
GenomeScope
5 days ago by
joshua.j.wright
▴ 10
0
votes
0
replies
83
views
Toxinpred 3.0 tool
peptide
protein
toxin
toxicity
updated 4 days ago by
zx8754
11k • written 5 days ago by
Saurabh
• 0
0
votes
0
replies
77
views
Troubleshooting a REGENIE sex-stratified GWAS
GWAS
REGENIE
19 hours ago by
s.may-wilson
▴ 40
0
votes
0
replies
74
views
How can validate hub genes or significant factors using area under the ROC curve (AUC)?
R
AUC
genes
hub
validation
4 days ago by
wyt1995
▴ 30
0
votes
0
replies
72
views
Remove SNPs based on MAF in Fst analysis
SNP
MAF
Fst
Popgenome
17 hours ago by
kopelol
▴ 20
0
votes
0
replies
69
views
Genotype simulation
gwas
simulation
sim1000
updated 16 hours ago by
Ram
43k • written 16 hours ago by
Eliza
▴ 30
0
votes
0
replies
67
views
Limma contrasts - difference between single and multiple concurrent contrasts results
R
limma
updated 14 hours ago by
Ram
43k • written 14 hours ago by
shasabhi1
• 0
0
votes
0
replies
61
views
Evaluating MAST model fit using AIC
cell
single
MAST
scRNA
transcriptomics
12 hours ago by
mhale
• 0
0
votes
0
replies
59
views
Tabula Sapiens and scanpy normalised expression data
scanpy
scRNA-seq
10x
normalisation
updated 15 hours ago by
Ram
43k • written 16 hours ago by
matt.a.bennett25890
• 0
0
votes
1
reply
59
views
library(scater)
sce
scRNASeq
scater
updated 3 hours ago by
Mensur Dlakic
★ 26k • written 4 hours ago by
Nitin
• 0
0
votes
1
reply
23
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq
GTEx
cram
updated 35 minutes ago by
Pierre Lindenbaum
160k • written 51 minutes ago by
Vullnet
• 0
1
vote
0
replies
4
views
ENVO Ontology to Annotate Plain Text
natural
language
NL
ontology
envo
3 minutes ago by
marie.harmel
▴ 10
81 results • Page
2 of 2
Recent Votes
Answer: Seurat 5 integration
Comment: scRNAseq normalization
Answer: scRNAseq normalization
Answer: scRNAseq normalization
A: Using A Variable As A Blocking Factor Vs Putting It As A Term In The Model Formu
Answer: Before or after LD clumping for PRS calculation in GWAS
Comment: CAZy database has multiple family sequence...
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Comment: scRNAseq normalization
by
sarahmanderni
▴ 100
Thanks for the response! I also was wondering to ask if you have found the log-norm also working fine in terms of downstream analysis like …
Answer: Subsetting Seurat object based on list of cell barcodes
by
fracarb8
★ 1.5k
`subset(seurat.obj_combined, cells = all_good_cells_rhemac10$V1)` You need to pass `cells` not `subset`. From the documentation: sub…
Answer: TCGA UUIDS to TCGA barcode (SampleID) in R
by
aUser
▴ 30
Great solutions on this page, the old web page has been replace with new one, so you need to use the new link, and it will work: old lin…
Comment: Issues With Cram -> Fastq from GTEx v8 WGS
by
Pierre Lindenbaum
160k
unless your cram in sorted on query rather than on coordinate, your cram must be first sort processed with collate: https://twitter.com/lh…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
Pierre Lindenbaum
160k
remove the spaces from your "chrom" key variableStep chrom=NT_173277 span=5 or may be quote the chrom variableStep chrom="NT_173277.1 C…
Comment: DEG (Differential expression gene) analysis
by
dsull
★ 5.6k
Well, I guess expression could be measured from the DNA indirectly such as with RNA Pol II binding to DNA via ChIP-seq but then the OP shou…
Answer: DEG (Differential expression gene) analysis
by
dsull
★ 5.6k
What exactly is "DNA-level DEG"? That makes zero sense. DEG = Differential **EXPRESSION** of genes. In any case, for RNA sequencing data, …
Answer: Biobambam vs Picard in RNA Sequencing Analysis for BAM to FASTQ
by
Zhenyu Zhang
★ 1.1k
Let me say even if you had used the exactly same bioinformatics steps, you will still have batch efforts from sample collection, storage an…
Comment: Before or after LD clumping for PRS calculation in GWAS
by
경준
▴ 20
1. I think i misunderstood logistic regression of association test. Now I understand. 2. you're right. Thank you for your helpful reply sam…
Comment: library(scater)
by
Mensur Dlakic
★ 26k
> I am not able to install the package scater as per the webpage I urge you to read back what you wrote and think whether you'd be able to…
Comment: How to corrected test statistics based on the LDSC intercept?
by
Isaac
• 0
Thank you very much!
Comment: Transcription Start Site
by
Ming Tommy Tang
★ 3.8k
you can use bioconductor as shown in this post using Genomicanges https://support.bioconductor.org/p/46508/
Comment: scRNAseq normalization
by
Ming Tommy Tang
★ 3.8k
To be honest, I really do not use SCT, and use log normalization all the time...
Comment: Subsetting Seurat object based on list of cell barcodes
by
Ming Tommy Tang
★ 3.8k
index<- rownames(seurat.obj_combined) %in% all_good_cells_rhemac10$V1 seurat.obj_combined[index, ] should do the trick
Comment: Average expression of a sample in single-cell data
by
dsull
★ 5.6k
Well, if you're only sequencing the very end (the 3' end) of transcripts, how are you going to detect any of the splice junctions that appe…
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