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54 results • Page
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34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 2 hours ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
3
votes
10
replies
628
views
t-test in two groups, multiple rows
R
t-test
11 hours ago by
sooni
▴ 20
3
votes
7
replies
1.2k
views
7 follow
Transcription Start Site
TSS
updated 7 hours ago by
Ming Tommy Tang
★ 3.8k • written 23 months ago by
Fatemeh Nabizadeh
▴ 10
0
votes
6
replies
461
views
How to corrected test statistics based on the LDSC intercept?
LDSC
intercept
7 hours ago by
Isaac
• 0
3
votes
5
replies
193
views
scRNAseq normalization
scRNA-seq
SCT
updated 1 hour ago by
ATpoint
81k • written 16 hours ago by
sarahmanderni
▴ 100
0
votes
4
replies
224
views
Expert Guidance Required for De Novo Transcriptome Analysis
Transcriptome
De-novo
updated 8 hours ago by
Doomhammer
• 0 • written 23 hours ago by
ben@f
▴ 10
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
0
votes
4
replies
231
views
blastn: 2.2.31+ Package: blast 2.2.31, build Jun 2 2015 10:47:46
blastn
blast
ubuntu
updated 18 hours ago by
SequenceServer
▴ 140 • written 1 day ago by
Luca
• 0
0
votes
4
replies
197
views
error in wigToBigWig while converting mappability to bedgraph
mappability
gem
bedgraph
wigToBigWig
2 hours ago by
Dora
▴ 10
4
votes
4
replies
206
views
Differential express genes in imbalance groups
Limma
10 hours ago by
Chris
▴ 260
1
vote
4
replies
232
views
BLAST parameters for sequences with high similarity
BLAST
Sanger
16S
v4
miseq
updated 23 hours ago by
GenoMax
140k • written 6 days ago by
behzad.karkaria
• 0
1
vote
3
replies
209
views
How to predict the affinity between Protein and RNA?
Protein-RNAinteractions
prediction
deeplearning
updated 22 hours ago by
dthorbur
★ 1.6k • written 4 days ago by
Alex
• 0
0
votes
3
replies
134
views
Haddock 2.4
Protein
Docking
1 hour ago by
Preeti
• 0
1
vote
3
replies
358
views
Does the order of the batch variable matter in Limma design matrix?
Batch
updated 5 hours ago by
Gordon Smyth
★ 6.9k • written 21 days ago by
CTLong
▴ 90
1
vote
3
replies
196
views
Average expression of a sample in single-cell data
single-cell
rna-seq
updated 7 hours ago by
dsull
★ 5.6k • written 21 hours ago by
newuser2024
• 0
0
votes
2
replies
128
views
Beagle Phasing and Imputation
imputation
phasing
beagle
2 hours ago by
Duarte Molha
▴ 240
0
votes
2
replies
172
views
data background noise
noise
data
17 hours ago by
marco.barr
▴ 30
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
4
votes
2
replies
136
views
Problem with .bed file
cygwin64
bed
PLINK
updated 15 hours ago by
Ram
43k • written 19 hours ago by
Dinmukhamed
• 0
0
votes
2
replies
113
views
Subsetting Seurat object based on list of cell barcodes
seurat
updated 2 hours ago by
fracarb8
★ 1.5k • written 12 hours ago by
bgbs
• 0
4
votes
2
replies
236
views
Before or after LD clumping for PRS calculation in GWAS
GWAS
4 hours ago by
경준
▴ 20
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
84
views
DEG (Differential expression gene) analysis
DEG
R
updated 3 hours ago by
dsull
★ 5.6k • written 4 hours ago by
sooni
▴ 20
1
vote
2
replies
357
views
(ERR): "GRCh38_noalt_as" does not exist or is not a Bowtie 2 index Exiting now ...
alignment
genomics
bowtie
bowtie2
updated 19 hours ago by
Ram
43k • written 19 days ago by
Song
• 0
0
votes
2
replies
157
views
calculating mean fragment length from CollectInsertSizeMetrics(Picard) output
count2fpkm
22 hours ago by
Niharika
• 0
0
votes
2
replies
134
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
28 minutes ago by
Learner
• 0
1
vote
2
replies
240
views
Trim Galore: Automatic detection of adapters
trimgalore
14 hours ago by
Daniel
▴ 30
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
1
reply
176
views
compareCluster's enrichGO difference in results when stating ont = "ALL" vs NULL
enrichGO
clusterProfiler
updated 19 hours ago by
Dunois
★ 2.5k • written 1 day ago by
TIANTHING JESTLIN
• 0
1
vote
1
reply
213
views
Compute p-value, having log fold change
p-value
fold-change
updated 18 hours ago by
Ram
43k • written 2 days ago by
Ngrin
• 0
0
votes
1
reply
178
views
Are there any tools for mutational analysis of viruses?
virus
updated 18 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 18 hours ago by
Ram
43k • written 2 days ago by
bioinfo_enthusiast
• 0
1
vote
1
reply
125
views
Seurat 5 integration
integration
seurat
updated 15 hours ago by
jared.andrews07
★ 16k • written 18 hours ago by
sarahmanderni
▴ 100
2
votes
1
reply
105
views
basal gene expression level
RNA-Seq
updated 14 hours ago by
LChart
3.8k • written 15 hours ago by
Francois Piumi
▴ 40
0
votes
1
reply
494
views
Downloading epigenetic and mutation data of specific TCGA BRCA samples
Mutation
RNA-Seq
TCGA
updated 9 hours ago by
aUser
▴ 30 • written 2.6 years ago by
Soura
• 0
0
votes
1
reply
164
views
Is it better to pool samples prior to running deseq2, or should the algorithm be run separately for every pool?
deseq2
RNA-seq
updated 8 hours ago by
swbarnes2
14k • written 11 hours ago by
Shelby
• 0
1
vote
1
reply
110
views
turning old shell ncbi querys into url querys
eutils
ncbi
updated 23 hours ago by
GenoMax
140k • written 1 day ago by
Guelakais
• 0
0
votes
1
reply
103
views
Biobambam vs Picard in RNA Sequencing Analysis for BAM to FASTQ
RNA-seq
Biobambam
Picard
updated 4 hours ago by
Zhenyu Zhang
★ 1.1k • written 14 hours ago by
kcarey
• 0
0
votes
1
reply
46
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq
GTEx
cram
updated 2 hours ago by
Pierre Lindenbaum
160k • written 3 hours ago by
Vullnet
• 0
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
0
votes
1
reply
36
views
why there is an asterisk symbol at the end of each proteins sequences offasta files in the Breaker3 output FASTA file?
gtf
breaker3
protein-seq
51 minutes ago by
mathavanbioinfo
▴ 70
0
votes
0
replies
64
views
Evaluating MAST model fit using AIC
cell
single
MAST
scRNA
transcriptomics
14 hours ago by
mhale
• 0
0
votes
0
replies
69
views
Limma contrasts - difference between single and multiple concurrent contrasts results
R
limma
updated 16 hours ago by
Ram
43k • written 17 hours ago by
shasabhi1
• 0
1
vote
0
replies
17
views
ENVO Ontology to Annotate Plain Text
natural
language
NL
ontology
envo
2 hours ago by
marie.harmel
▴ 10
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 18 hours ago by
matt.a.bennett25890
• 0
0
votes
0
replies
16
views
adding new assemblies to previously built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
1 hour ago by
b.contreras.moreira
▴ 10
0
votes
0
replies
75
views
Remove SNPs based on MAF in Fst analysis
SNP
MAF
Fst
Popgenome
20 hours ago by
kopelol
▴ 20
0
votes
0
replies
71
views
Genotype simulation
gwas
simulation
sim1000
updated 18 hours ago by
Ram
43k • written 18 hours ago by
Eliza
▴ 30
0
votes
0
replies
145
views
Anvio HMM source campbell_et_al
anvio
updated 18 hours ago by
Ram
43k • written 3 days ago by
Hayler Edu
▴ 40
54 results • Page
1 of 2
Recent Votes
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
Answer: Seurat 5 integration
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Devon Ryan
104k
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▴ 60
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★ 3.8k
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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…
Answer: 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…
Answer: Haddock 2.4
by
Preeti
• 0
I want to know that which results from haddock are good like I got highest haddock score of -75 .....is it a good haddock score or not
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…
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