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81 results • Page
2 of 2
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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
59
views
Tabula Sapiens and scanpy normalised expression data
scanpy
scRNA-seq
10x
normalisation
updated 16 hours ago by
Ram
43k • written 16 hours ago by
matt.a.bennett25890
• 0
0
votes
2
replies
172
views
data background noise
noise
data
15 hours ago by
marco.barr
▴ 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
3
replies
188
views
Average expression of a sample in single-cell data
single-cell
rna-seq
updated 5 hours ago by
dsull
★ 5.6k • written 19 hours ago by
newuser2024
• 0
0
votes
1
reply
59
views
library(scater)
sce
scRNASeq
scater
updated 4 hours ago by
Mensur Dlakic
★ 26k • written 4 hours ago by
Nitin
• 0
0
votes
1
reply
24
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq
GTEx
cram
updated 45 minutes ago by
Pierre Lindenbaum
160k • written 1 hour ago by
Vullnet
• 0
0
votes
1
reply
230
views
I can't add VAF from population for all of my variants from VCF file
vaf
vcf
genomics
gnomad
allelicfrequency
updated 2 days ago by
Arton
• 0 • written 4 days ago by
Samuel
▴ 20
0
votes
7
replies
423
views
Using VEP annotation output as the input for a second VEP annotation
VCF
VEP
Annotation
updated 6 days ago by
Ram
43k • written 6 weeks ago by
Arton
• 0
0
votes
0
replies
119
views
HADDOCK 2.4
Protein
Docking
6 days ago by
Preeti
• 0
0
votes
5
replies
342
views
Same NCBI IDs for different Ensembl IDs / Multiple NCBI IDs for an Ensembl ID
KEGG
ENTREZ
ENSEMBL
6 days ago by
Maxwell
• 0
0
votes
1
reply
138
views
SNP and Genes position matching dataframes in R
R
dataframe
updated 5 days ago by
dthorbur
★ 1.6k • written 5 days ago by
QX
• 0
0
votes
0
replies
96
views
Issue to run gatk4 spark
gatk
spark
5 days ago by
Mojtaba
• 0
0
votes
1
reply
150
views
Alignment tool of repeat expansion detection
STR
NGS
readexpansion
updated 5 days ago by
Jesse
▴ 740 • written 6 days ago by
adarsh_pp
▴ 40
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
2
replies
179
views
Is there a program that can predict the sequence of an organisms telomeres just from raw sequencing reads
telomeres
genomics
sequencing
5 days ago by
Mark
• 0
0
votes
10
replies
735
views
Problem running scPred
scPred
scPredict
updated 5 days ago by
Ram
43k • written 10 weeks ago by
Nitin
• 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
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
0
replies
99
views
What to do with multiple genes in ballgown?
STAR
ballgown
DESeq2
5 days ago by
markusz
▴ 10
0
votes
1
reply
132
views
Longitudinal microbiome study - Pooling of data?
longitudinal-microbiome-study
statistics
updated 5 days ago by
Chris Dean
▴ 390 • written 5 days ago by
laura_g
• 0
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
5 days ago by
wyt1995
▴ 30
0
votes
0
replies
83
views
Toxinpred 3.0 tool
peptide
protein
toxin
toxicity
updated 5 days ago by
zx8754
11k • written 5 days ago by
Saurabh
• 0
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
448
views
Looking for guidance on Microbial Association Networks (MANs) Inference with samples from different metagenomics/metatranscriptomics studies
microbialassociationnetworks
metatranscriptomics
metagenomics
netowrkbiology
4 days ago by
sebasar1245
• 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
118
views
Music2 human to mouse deconvolution
deconvolution
liftover
music2
4 days ago by
rbronste
▴ 420
0
votes
2
replies
171
views
Weird Basecalled reads PHRED quality plot from pycoQC
pycoQC
nanopore
sequencing
4 days ago by
njornet
▴ 10
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
8
replies
1.4k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools
MarkDuplicates
updated 4 days ago by
xiangbinruan
• 0 • written 18 months ago by
Phoebe Magdy
• 0
81 results • Page
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Recent Votes
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▴ 240
Hi @lchart Thank you for your answer. I coded my male sample as biallelelic homozygous as i was aware of limitations for allosomes.…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
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And I also change the chrom name in the .sizes file. That works perfect. Thank you very much!
Comment: scRNAseq normalization
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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
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`subset(seurat.obj_combined, cells = all_good_cells_rhemac10$V1)` You need to pass `cells` not `subset`. From the documentation: sub…
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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
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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…
Answer: error in wigToBigWig while converting mappability to bedgraph
by
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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
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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, …
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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
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★ 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!
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Ming Tommy Tang
★ 3.8k
you can use bioconductor as shown in this post using Genomicanges https://support.bioconductor.org/p/46508/
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To be honest, I really do not use SCT, and use log normalization all the time...
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