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491 results • Page
3 of 10
Sort: Votes
Rank
Views
Votes
Replies
1
vote
1
reply
408
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
8 days ago by
renan.igor
• 0
1
vote
3
replies
391
views
multiple sequence alignment
BLAST
multiple-sequence-alignment
clustal-omega
MSA
updated 19 days ago by
Ram
43k • written 22 days ago by
catherinemaria2728
• 0
1
vote
3
replies
352
views
how to do the repeatability filtering of vcf files?
snp
vcf.
updated 26 days ago by
Pierre Lindenbaum
161k • written 27 days ago by
Max
• 0
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 9 days ago by
Ram
43k • written 6.6 years ago by
Alternative
▴ 270
1
vote
2
replies
222
views
convert a seurat object to expressionset
Seurat
16 days ago by
Bine
▴ 60
1
vote
2
replies
291
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
11 days ago by
bp22
▴ 80
1
vote
1
reply
193
views
Tool for gene function identification
Gene-Function
updated 25 days ago by
Ram
43k • written 26 days ago by
Estevão
• 0
1
vote
1
reply
226
views
Retrieve a % coverage for each transcript
RNA-seq
updated 10 days ago by
Ram
43k • written 10 days ago by
jammydodger123456
▴ 40
1
vote
2
replies
207
views
In need of help with my RNA velocity trajectory inference pipeline!
RNAvelocity
19 days ago by
phhelou5
• 0
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 5 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
1
reply
181
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 11 days ago by
dsull
★ 5.9k • written 11 days ago by
niruf
• 0
1
vote
4
replies
282
views
Removing batch effect using combat-seq
batch
effect
RNA-Seq
combat-seq
updated 26 days ago by
BioinfGuru
★ 1.7k • written 26 days ago by
Netanel
• 0
1
vote
1
reply
176
views
Failed to download data from EBI with ascp
EBI
aspera
updated 16 days ago by
GenoMax
141k • written 16 days ago by
biock
▴ 60
1
vote
3
replies
264
views
some error in building kraken2 database
metagenome
kraken2
3 days ago by
Art1ess
• 0
1
vote
3
replies
1.7k
views
Using Nanoplot to asses quality of ONT data
ONT
Long-read-sequencing
NanoPlot
updated 22 days ago by
Ram
43k • written 2.3 years ago by
matt81rd
▴ 10
1
vote
0
replies
97
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
1 day ago by
KABILAN
▴ 50
1
vote
2
replies
270
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
11 days ago by
bioinfo
▴ 150
1
vote
3
replies
260
views
CCA with random effects model
CCA
updated 25 days ago by
dariober
14k • written 26 days ago by
leranwangcs
▴ 120
1
vote
5
replies
345
views
samtools filtering
samtools
updated 16 days ago by
jkbonfield
★ 1.2k • written 24 days ago by
sansan_96
▴ 80
1
vote
2
replies
319
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 12 days ago by
Istvan Albert
100k • written 13 days ago by
Jiang
• 0
1
vote
0
replies
157
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 16 days ago by
Ram
43k • written 16 days ago by
ian.will
▴ 30
1
vote
2
replies
239
views
permutation test in edgeR
rna-seq
edgeR
updated 5 days ago by
Gordon Smyth
★ 7.0k • written 19 days ago by
Netanel
• 0
1
vote
1
reply
465
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 19 days ago by
chrchang523
10k • written 19 days ago by
dsbusiness135
▴ 10
1
vote
2
replies
331
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 24 days ago by
jkbonfield
★ 1.2k • written 6 weeks ago by
geocarvalho
▴ 360
1
vote
0
replies
143
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 12 days ago by
Ram
43k • written 12 days ago by
Oscar
▴ 10
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 10 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
1
vote
0
replies
191
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
29 days ago by
Shicheng Guo
★ 9.4k
1
vote
1
reply
227
views
Cell type classification using an integrated reference
scRNAseq
updated 26 days ago by
bk11
★ 2.4k • written 27 days ago by
kayah
• 0
1
vote
2
replies
823
views
Replacing default numbers with geneNames in enhancedVolcano
EnhancedVolcano
updated 25 days ago by
Ram
43k • written 2.6 years ago by
Mohan
• 0
1
vote
3
replies
354
views
Ensembl gene id conversion
biomart
ensembl
updated 11 days ago by
ATpoint
82k • written 13 days ago by
naveedhasan2000
• 0
1
vote
1
reply
196
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
12 days ago by
CTLong
▴ 110
1
vote
2
replies
924
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 22 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
1
vote
1
reply
247
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 15 days ago by
Ram
43k • written 15 days ago by
Fish
• 0
1
vote
3
replies
281
views
True variants selection
vcf
bcftools
updated 15 days ago by
dthorbur
★ 1.9k • written 16 days ago by
maevalefeuvre
• 0
1
vote
1
reply
170
views
Failed kmer content
kmer
illumina
ngs
updated 4 days ago by
Ram
43k • written 4 days ago by
Kasturi
• 0
1
vote
0
replies
368
views
Differential expression analysis on multiple integrated datasets
microarray
Z-score
limma
differential-gene-expression
meta-analysis
updated 18 days ago by
Ram
43k • written 2.4 years ago by
michael.s
▴ 10
1
vote
4
replies
815
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
18 days ago by
Hyper_Odin
▴ 310
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva
batch-effect
RRBS
updated 11 days ago by
Ram
43k • written 7.1 years ago by
mrodrigues.fernanda
▴ 50
0
votes
0
replies
106
views
Databases with GoF (Gain of Function) annotations.
gof
lof
gain-of-function
18 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
98
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
4 days ago by
ohtang7
▴ 40
0
votes
2
replies
379
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
8 days ago by
Ashok
• 0
0
votes
0
replies
254
views
batch correction: cds from seurat
batch-correction
R
seurat
monocle3
cds
updated 18 days ago by
Ram
43k • written 18 days ago by
sooni
▴ 20
0
votes
1
reply
244
views
eQTL analysis of GWAS summary statistics, missing GT values
Genomics
eQTL
GWAS
updated 22 days ago by
Ram
43k • written 12 weeks ago by
Orlando
• 0
0
votes
0
replies
127
views
How to annotate pairwise p value from limma (3 groups) in a combine multiple boxplot?
limma
boxplot
18 days ago by
Chris
▴ 260
0
votes
0
replies
104
views
How to extract BED-format annotation tracks for the newly inserted segments
bed
mauve
updated 25 days ago by
Ram
43k • written 25 days ago by
FZ
• 0
0
votes
0
replies
2.8k
views
TCGA RNAseqVer2 batch effects
TCGA
RNA-Seq
batch-effect
updated 10 days ago by
Ram
43k • written 8.6 years ago by
annadv
• 0
0
votes
0
replies
102
views
RNA-seq: full length gene
RNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
Nargis
• 0
0
votes
0
replies
142
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
2 days ago by
4fzcgueyp5
• 0
0
votes
0
replies
143
views
GWAS Phenotypes
GWAS
11 days ago by
solomoncharles77
▴ 90
0
votes
2
replies
239
views
Annovar using R package
Annovar
gnomAD
R
2 days ago by
DKA
▴ 40
491 results • Page
3 of 10
Recent Votes
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
correcting for a batch in DESeq2
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I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated
by
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★ 5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
Comment: NGS forensics: how to know if data is fabricated
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> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
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Thank you for your valuable suggestion!
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My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
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