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24 results • Page
1 of 1
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Rank
Views
Votes
Replies
0
votes
0
replies
7
views
TensorQTL Mapping - permutation p values for all associations
permutation
TensorQTL
6 minutes ago by
Paula
• 0
0
votes
0
replies
14
views
Long branch lengths, low bootstrap values and misalignments
mafft
muscle
iqtree
1 hour ago by
samyu.senthil
• 0
0
votes
2
replies
136
views
Haddock 2.4
Protein
Docking
1 hour ago by
Preeti
• 0
0
votes
0
replies
17
views
adding new assemblies to previously built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
1 hour ago by
b.contreras.moreira
▴ 10
1
vote
0
replies
18
views
ENVO Ontology to Annotate Plain Text
natural
language
NL
ontology
envo
2 hours ago by
marie.harmel
▴ 10
0
votes
1
reply
48
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq
GTEx
cram
updated 3 hours ago by
Pierre Lindenbaum
160k • written 3 hours ago by
Vullnet
• 0
0
votes
1
reply
67
views
library(scater)
sce
scRNASeq
scater
updated 6 hours ago by
Mensur Dlakic
★ 26k • written 6 hours ago by
Nitin
• 0
0
votes
0
replies
64
views
Evaluating MAST model fit using AIC
cell
single
MAST
scRNA
transcriptomics
15 hours ago by
mhale
• 0
0
votes
0
replies
69
views
Limma contrasts - difference between single and multiple concurrent contrasts results
R
limma
updated 17 hours ago by
Ram
43k • written 17 hours ago by
shasabhi1
• 0
0
votes
0
replies
72
views
Genotype simulation
gwas
simulation
sim1000
updated 18 hours ago by
Ram
43k • written 18 hours ago by
Eliza
▴ 30
0
votes
0
replies
67
views
Tabula Sapiens and scanpy normalised expression data
scanpy
scRNA-seq
10x
normalisation
updated 18 hours ago by
Ram
43k • written 19 hours ago by
matt.a.bennett25890
• 0
0
votes
0
replies
75
views
Remove SNPs based on MAF in Fst analysis
SNP
MAF
Fst
Popgenome
20 hours ago by
kopelol
▴ 20
1
vote
1
reply
101
views
Troubleshooting a REGENIE sex-stratified GWAS
GWAS
REGENIE
updated 1 hour ago by
Corentin
▴ 600 • written 22 hours ago by
s.may-wilson
▴ 50
1
vote
3
replies
197
views
Average expression of a sample in single-cell data
single-cell
rna-seq
updated 8 hours ago by
dsull
★ 5.6k • written 22 hours ago by
newuser2024
• 0
0
votes
2
replies
154
views
nf-core/rnaseq, problem with ensembl reference
nfcore
nextflow
ensembl
rnaseq
19 hours ago by
Filip
• 0
0
votes
2
replies
157
views
calculating mean fragment length from CollectInsertSizeMetrics(Picard) output
count2fpkm
23 hours ago by
Niharika
• 0
0
votes
2
replies
167
views
FASTA/FASTQ files of fetal Aneuploids
nipt
23 hours ago by
lolbye_1
• 0
1
vote
2
replies
209
views
Upset plot
upsetplot
21 hours ago by
Chris
▴ 260
0
votes
1
reply
178
views
Are there any tools for mutational analysis of viruses?
virus
updated 19 hours ago by
Ram
43k • written 2 days ago by
joey
▴ 10
1
vote
1
reply
167
views
Seeking help with Tcga Target Gtex Expected Count Data
R
TCGA
gTEX
updated 19 hours ago by
Ram
43k • written 2 days ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
145
views
Anvio HMM source campbell_et_al
anvio
updated 19 hours ago by
Ram
43k • written 3 days ago by
Hayler Edu
▴ 40
1
vote
3
replies
209
views
How to predict the affinity between Protein and RNA?
Protein-RNAinteractions
prediction
deeplearning
updated 23 hours ago by
dthorbur
★ 1.6k • written 4 days ago by
Alex
• 0
0
votes
2
replies
172
views
data background noise
noise
data
17 hours ago by
marco.barr
▴ 30
1
vote
4
replies
1.1k
views
NGS/GATK pipeline returns too many variants
NGS
WES
GATK
Mutect
updated 1 hour ago by
dhruti
• 0 • written 3.1 years ago by
dodausp
▴ 180
24 results • Page
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Recent Votes
Comment: BAM to CRAM and BAM recover with smaller size
Comment: Average expression of a sample in single-cell data
A: Normalize FPKM values for cross-sample comparisons?
Answer: ColabFold
C: How To Convert Arabidopsis Gene Id To Ncbi Geneid, Ncbi-Gi Or Uniprot?
Troubleshooting a REGENIE sex-stratified GWAS
ENVO Ontology to Annotate Plain Text
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Recent Awards •
All
Scholar
to
Devon Ryan
104k
Scholar
to
inedraylig
▴ 60
Teacher
to
Ming Tommy Tang
★ 3.8k
Popular Question
to
aUser
▴ 30
Teacher
to
Gordon Smyth
★ 6.9k
Popular Question
to
H.Hasani
▴ 990
Popular Question
to
kcarey
• 0
Recent Replies
Answer: Deeptools scale issue for plotHeatmap
by
Learner
• 0
Hi Devon, Thanks a lot for the reply. DNA methylation file has 19466838 lines while domains has 92409 lines.
Answer: why there is an asterisk symbol at the end of each proteins sequences offasta fi
by
Juke34
8.5k
It corresponds to stop codon but in theory GTF format does not have stop codon in CDS. Keep in mind that it exists stop codon reading th…
Comment: scRNAseq normalization
by
ATpoint
81k
That is an entirely different analysis and depends on the testing Framework. If you use the commonly-used Wilcox test or something like lim…
Comment: Haddock 2.4
by
Preeti
• 0
i have three different runs with haddock score of -75, -68, -61 . Which one is better among these( molecule 1 is same in all three ,only mo…
Comment: NGS/GATK pipeline returns too many variants
by
dhruti
• 0
@dodausp Did you ever find a reason for this? I am having the same problem
Comment: Troubleshooting a REGENIE sex-stratified GWAS
by
Corentin
▴ 600
Sex chromosomes are always a bit tricky to handle in associations studies. How many male cases and male controls you have for this phenoty…
Comment: Beagle Phasing and Imputation
by
Duarte Molha
▴ 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
Dora
▴ 10
And I also change the chrom name in the .sizes file. That works perfect. Thank you very much!
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…
Answer: 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, …
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