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348 results • Page
3 of 7
Sort: Rank
Rank
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Votes
Replies
0
votes
1
reply
185
views
PEAR seems to have sense to me
PEAR
updated 7 days ago by
GenoMax
140k • written 7 days ago by
ManuelDB
▴ 80
0
votes
1
reply
170
views
Interprete plot of dispersion estimation by DESeq2
dispersion
DEXseq
DESeq2
updated 7 days ago by
Pierre Lindenbaum
160k • written 7 days ago by
tien
▴ 10
0
votes
1
reply
157
views
Adding gene to GRange objects with single base
GRanges
genomics
updated 7 days ago by
ATpoint
81k • written 8 days ago by
QX
• 0
0
votes
0
replies
149
views
Change orig.ident column in seurat meta.data to match cell barcode sample prefixes
seurat
8 days ago by
bgbs
• 0
0
votes
0
replies
137
views
Motif analysis by HOMER
Homer
8 days ago by
daffodil
▴ 10
1
vote
2
replies
544
views
Applicability of the SoupX ambient mRNA decontamination technique to fixed and/or multiplexed scRNAseq experiments
SoupX
scRNA-seq
8 days ago by
e.r.zakiev
▴ 170
0
votes
0
replies
133
views
DADA2 truncLen value
metabarcoding
phyloseq
DADA2
illumina
9 days ago by
Bioinfo
▴ 20
0
votes
1
reply
175
views
Resources regarding Proteomics (In-Silico)
proteomics
docking
protein
molecular-simulation
updated 9 days ago by
Ram
43k • written 9 days ago by
Saurabh
• 0
1
vote
0
replies
142
views
TensorQTL Mapping - permutation p values for all associations
permutation
TensorQTL
9 days ago by
Paula
▴ 10
0
votes
5
replies
403
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
5 days ago by
Learner
• 0
1
vote
5
replies
408
views
Haddock 2.4
Protein
Docking
updated 8 days ago by
dthorbur
★ 1.7k • written 10 days ago by
Preeti
• 0
1
vote
0
replies
110
views
ENVO Ontology to Annotate Plain Text
natural
language
NL
ontology
envo
9 days ago by
marie.harmel
▴ 10
0
votes
1
reply
158
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq
GTEx
cram
updated 9 days ago by
Pierre Lindenbaum
160k • written 9 days ago by
Vullnet
• 0
0
votes
0
replies
115
views
Evaluating MAST model fit using AIC
cell
single
MAST
scRNA
transcriptomics
9 days ago by
mhale
• 0
0
votes
0
replies
125
views
Limma contrasts - difference between single and multiple concurrent contrasts results
R
limma
updated 9 days ago by
Ram
43k • written 9 days ago by
shasabhi1
• 0
0
votes
0
replies
125
views
Genotype simulation
gwas
simulation
sim1000
updated 9 days ago by
Ram
43k • written 9 days ago by
Eliza
▴ 30
0
votes
0
replies
107
views
Remove SNPs based on MAF in Fst analysis
SNP
MAF
Fst
Popgenome
10 days ago by
kopelol
▴ 20
1
vote
1
reply
175
views
Troubleshooting a REGENIE sex-stratified GWAS
GWAS
REGENIE
updated 9 days ago by
Corentin
▴ 600 • written 10 days ago by
s.may-wilson
▴ 50
1
vote
3
replies
254
views
Average expression of a sample in single-cell data
single-cell
rna-seq
updated 9 days ago by
dsull
★ 5.7k • written 10 days ago by
newuser2024
• 0
0
votes
2
replies
233
views
nf-core/rnaseq, problem with ensembl reference
nfcore
nextflow
ensembl
rnaseq
9 days ago by
Filip
• 0
0
votes
2
replies
195
views
FASTA/FASTQ files of fetal Aneuploids
nipt
10 days ago by
lolbye_1
• 0
0
votes
0
replies
125
views
comparing sc-seq combination and bulk-sequencing
bulk-sequencing
sc-sequencing
10 days ago by
润达
• 0
0
votes
1
reply
172
views
BRIG coverage.graph issues
BRIG
sam
updated 10 days ago by
Pierre Lindenbaum
160k • written 10 days ago by
dlera.lozano
• 0
0
votes
0
replies
129
views
How to generate a comparative map using CGview?
genome
map
CGView
11 days ago by
marongiu.luigi
▴ 710
0
votes
0
replies
144
views
Advice on telling if two SNPs are on the same haplotype
ldpair
halplotype
co-occurance
gnomad
snp
11 days ago by
amy__
▴ 160
1
vote
2
replies
440
views
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
RNA-seq
DESeq
EdgeR
Batch-effect
DEGs
10 days ago by
BioinfGuru
★ 1.6k
1
vote
2
replies
238
views
Upset plot
upsetplot
10 days ago by
Chris
▴ 260
0
votes
1
reply
205
views
Are there any tools for mutational analysis of viruses?
virus
updated 9 days ago by
Ram
43k • written 11 days ago by
joey
▴ 10
0
votes
1
reply
253
views
I can't add VAF from population for all of my variants from VCF file
vaf
vcf
genomics
gnomad
allelicfrequency
updated 11 days ago by
Arton
• 0 • written 14 days ago by
Samuel
▴ 20
0
votes
0
replies
141
views
Analyzing differentially methylated regions from Nanopore long read data?
bioinformatics
Long
read
sequencing
methylation
11 days ago by
Arton
• 0
2
votes
2
replies
292
views
Seeking help with Tcga Target Gtex Expected Count Data
R
TCGA
gTEX
4 days ago by
bioinfo_enthusiast
• 0
1
vote
0
replies
148
views
How should I regenotype VCFs using vg?
vg
11 days ago by
Ricky
▴ 10
1
vote
2
replies
243
views
What GC content should I expect?
RNA-seq
GC-content
updated 11 days ago by
ATpoint
81k • written 11 days ago by
BioinfGuru
★ 1.6k
0
votes
0
replies
136
views
stat test
stattest
chi2
updated 12 days ago by
GenoMax
140k • written 12 days ago by
NLL
• 0
0
votes
0
replies
162
views
Anvio HMM source campbell_et_al
anvio
updated 9 days ago by
Ram
43k • written 12 days ago by
Hayler Edu
▴ 40
0
votes
1
reply
224
views
Issue with bigWigSummary utility of Kent/UCSC utilities
bigWig
UCSC
updated 12 days ago by
Pierre Lindenbaum
160k • written 12 days ago by
eeb74
• 0
0
votes
1
reply
221
views
deepTools computeMatrix output import into R for enrichment calculations
R
deeptools
computeMatrix
deepTools
updated 12 days ago by
Pierre Lindenbaum
160k • written 12 days ago by
eeb74
• 0
1
vote
1
reply
243
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 12 days ago by
GenoMax
140k • written 12 days ago by
geocarvalho
▴ 360
0
votes
0
replies
155
views
admixfrog for high-coverage data
introgression
12 days ago by
gubrins
▴ 290
0
votes
1
reply
236
views
updateR() error
R
update
updated 10 days ago by
dthorbur
★ 1.7k • written 13 days ago by
marco.barr
▴ 30
0
votes
0
replies
163
views
Haplotype Phasing from Yeast strains
yeast
haplotype
phasing
13 days ago by
Sven K
• 0
0
votes
0
replies
171
views
cufflinks- cuffquant issue
cufflinks
13 days ago by
soyeon
• 0
2
votes
2
replies
262
views
compare dimplot(single cell)
DEG
scRNAseq
12 days ago by
kayah
• 0
1
vote
1
reply
234
views
--busco_db and --busco_seed_species with RNA-seq
RNA-seq
Funannotate
busco
13 days ago by
sansan_96
▴ 50
0
votes
0
replies
162
views
Computational Package to engage Type 2 Diabetes Knowledge Portal (T2DKP)
workflow
Package
13 days ago by
Shicheng Guo
★ 9.4k
0
votes
1
reply
199
views
Pathway activity in Bulk-RNA-SEQ analysis
R
RNA-seq
transcriptomics
updated 13 days ago by
jared.andrews07
★ 16k • written 13 days ago by
PBC
▴ 10
1
vote
1
reply
207
views
lncRNA and ncPEPs identification
lncRNA
updated 13 days ago by
Yahel
• 0 • written 15 days ago by
atharvakarkare14
▴ 10
0
votes
0
replies
128
views
Music2 human to mouse deconvolution
deconvolution
liftover
music2
14 days ago by
rbronste
▴ 420
0
votes
2
replies
196
views
Weird Basecalled reads PHRED quality plot from pycoQC
pycoQC
nanopore
sequencing
14 days ago by
njornet
▴ 10
0
votes
0
replies
136
views
computeGCBias outputs
GC
bam
deepTools
GCbias
13 days ago by
pablo
▴ 300
348 results • Page
3 of 7
Recent Votes
A: Read Duplicates
A: Read Duplicates
How can two contradicted gene sets be enriched in a cancer sample in GSEA analysis?
Comment: Only one read per run - Trying to use CellRangerv7
Comment: Interproscan taking so much time
Answer: Interproscan taking so much time
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
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Recent Awards •
All
Commentator
to
Devon Ryan
104k
Popular Question
to
amitpande74
▴ 20
Scholar
to
Pierre Lindenbaum
160k
Popular Question
to
beacamara
• 0
Popular Question
to
blur
▴ 280
Popular Question
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ATpoint
81k
Teacher
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Haci
▴ 550
Recent Replies
Comment: Normalization strategies for comparing mapped reads across samples in RNA-seq
by
Ram
43k
> TPM seems like a good method, but it may not be suitable here because it requires gene/transcript length. Also because TPM cannot be com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I did run the `JoinLayers()` even then it is not working, here is the output before and after ```r DefaultAssay(combined1) <- 'RNA' com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I tried that too. It did not work.
Comment: (sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
by
GenoMax
140k
Try SRA-explorer with search terms you want. Guide here: https://www.biostars.org/p/366721/ Check these portals: https://singlecell.broad…
Comment: Issue with making local BLAST database
by
Begonia_pavonina
▴ 140
Thank you @genomax, if I have well understood the `retmax` parameter and 10000 entries limitation are linked to the R package, and not to t…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you , this is my code : import sys import os import subprocess class FastpFiltering: def __init__(self, input_folder, fastp_ou…
Comment: Nanopore data filtering using fastp
by
GenoMax
140k
You can also use `reformat.sh` from [**BBMap suite**][1]. Look at sampling options. [1]: https://sourceforge.net/projects/bbmap/
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I was using it but the output file was too big pipe the output
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Share code and an example please.
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
I was using it but the output file was too big, so that I thought the vcf file was more efficient. But now I know that I can stop working o…
Comment: Interproscan taking so much time
by
Mohamed Abderrahmane
▴ 10
Thank you for your reply. I have just executed the computation with parallelization as you mentioned, and I will observe the differences. H…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Of course ... But as 'expected' the range `range=chr8:127794533-128101253` in the output sequence file belongs to: LF385466, LF385467, MA62…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
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