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531 results • Page
3 of 11
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1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 8 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
1
vote
2
replies
808
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 8 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
1
vote
2
replies
269
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 7 days ago by
Ram
43k • written 7 days ago by
aniigodwinn
• 0
1
vote
2
replies
258
views
Is it possible to see so little adipocyte in white adipose tissue?
scRNA-seq
29 days ago by
kayah
• 0
1
vote
4
replies
344
views
How to get human-mouse conservation score from UCSC
conservation
mouse
IGV
human
score
20 days ago by
diqixiaoyaoer
▴ 10
1
vote
1
reply
190
views
Tool for gene function identification
Gene-Function
updated 23 days ago by
Ram
43k • written 23 days ago by
Estevão
• 0
1
vote
2
replies
259
views
Deseq generating warning "the model matrix is not full rank"
deseq
updated 29 days ago by
bioruffo
▴ 40 • written 4 weeks ago by
MAPK2
▴ 40
1
vote
2
replies
166
views
alignment result
RNA-seq
samtools
hisat2
9 hours ago by
ahmad.sajad4541
• 0
1
vote
2
replies
217
views
convert a seurat object to expressionset
Seurat
14 days ago by
Bine
▴ 60
1
vote
3
replies
194
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
2 days ago by
WouterDeCoster
47k
1
vote
3
replies
1.7k
views
Using Nanoplot to asses quality of ONT data
ONT
Long-read-sequencing
NanoPlot
updated 19 days ago by
Ram
43k • written 2.3 years ago by
matt81rd
▴ 10
1
vote
1
reply
181
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 10 days ago by
GenoMax
141k • written 10 days ago by
eesiribloom
▴ 80
1
vote
1
reply
411
views
Long reads Annotation
long-reads
pacbio
updated 19 days ago by
Ram
43k • written 2.1 years ago by
Gerardo
• 0
1
vote
2
replies
242
views
What are crucial apps/ scripts for cancer genome/data analysis that can be set up as an web based app?
web
based
cancer
updated 23 days ago by
LauferVA
4.2k • written 24 days ago by
bartek
• 0
1
vote
2
replies
286
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
9 days ago by
bp22
▴ 80
1
vote
1
reply
412
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 7 days ago by
Chris
▴ 260
1
vote
1
reply
460
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 16 days ago by
chrchang523
10k • written 17 days ago by
dsbusiness135
▴ 10
1
vote
1
reply
819
views
Question for 3 prime bias in rna short read and long read (illumina, ont, pacbio)
rna-seq
short-read
long-read
updated 19 days ago by
Ram
43k • written 11 months ago by
shinyjj
▴ 50
1
vote
1
reply
175
views
Failed to download data from EBI with ascp
EBI
aspera
updated 14 days ago by
GenoMax
141k • written 14 days ago by
biock
▴ 60
1
vote
2
replies
314
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 9 days ago by
Istvan Albert
100k • written 11 days ago by
Jiang
• 0
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 2 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma
Batch-effect
MDS
Galaxy
updated 8 days ago by
Ram
43k • written 4.8 years ago by
sonayuv
• 0
1
vote
1
reply
223
views
Retrieve a % coverage for each transcript
RNA-seq
updated 7 days ago by
Ram
43k • written 7 days ago by
jammydodger123456
▴ 40
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 7 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
1
vote
0
replies
367
views
Differential expression analysis on multiple integrated datasets
microarray
Z-score
limma
differential-gene-expression
meta-analysis
updated 15 days ago by
Ram
43k • written 2.4 years ago by
michael.s
▴ 10
1
vote
2
replies
922
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 19 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
1
vote
3
replies
345
views
Ensembl gene id conversion
biomart
ensembl
updated 9 days ago by
ATpoint
82k • written 11 days ago by
naveedhasan2000
• 0
1
vote
2
replies
265
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
8 days ago by
bioinfo
▴ 150
1
vote
0
replies
155
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 14 days ago by
Ram
43k • written 14 days ago by
ian.will
▴ 30
1
vote
3
replies
253
views
CCA with random effects model
CCA
updated 23 days ago by
dariober
14k • written 23 days ago by
leranwangcs
▴ 120
1
vote
1
reply
38
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 57 minutes ago by
bk11
★ 2.3k • written 1 hour ago by
starswillfade
▴ 10
1
vote
4
replies
807
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
15 days ago by
Hyper_Odin
▴ 310
1
vote
1
reply
158
views
Failed kmer content
kmer
illumina
ngs
updated 2 days ago by
Ram
43k • written 2 days ago by
Kasturi
• 0
1
vote
4
replies
279
views
Removing batch effect using combat-seq
batch
effect
RNA-Seq
combat-seq
updated 23 days ago by
BioinfGuru
★ 1.7k • written 24 days ago by
Netanel
• 0
1
vote
5
replies
249
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 80
1
vote
0
replies
1.1k
views
interpretation of trajectory and batch effect
monocle3
batch-effect
trajectory
updated 16 days ago by
Ram
43k • written 3.5 years ago by
tushard1987
▴ 10
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva
batch-effect
RRBS
updated 8 days ago by
Ram
43k • written 7.1 years ago by
mrodrigues.fernanda
▴ 50
1
vote
1
reply
244
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 13 days ago by
Ram
43k • written 13 days ago by
Fish
• 0
1
vote
2
replies
325
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 22 days ago by
jkbonfield
★ 1.2k • written 5 weeks ago by
geocarvalho
▴ 360
1
vote
0
replies
158
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
14 days ago by
eesiribloom
▴ 80
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 9 days ago by
Ram
43k • written 9 days ago by
Oscar
▴ 10
1
vote
2
replies
228
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
★ 7.0k • written 17 days ago by
Netanel
• 0
1
vote
0
replies
184
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
27 days ago by
Shicheng Guo
★ 9.4k
1
vote
0
replies
149
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 27 days ago by
Ram
43k • written 28 days ago by
Tolga
▴ 30
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 8 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
1
vote
2
replies
202
views
In need of help with my RNA velocity trajectory inference pipeline!
RNAvelocity
16 days ago by
phhelou5
• 0
1
vote
1
reply
196
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
10 days ago by
CTLong
▴ 110
1
vote
3
replies
275
views
True variants selection
vcf
bcftools
updated 13 days ago by
dthorbur
★ 1.9k • written 14 days ago by
maevalefeuvre
• 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 6 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
1
vote
2
replies
821
views
Replacing default numbers with geneNames in enhancedVolcano
EnhancedVolcano
updated 23 days ago by
Ram
43k • written 2.6 years ago by
Mohan
• 0
531 results • Page
3 of 11
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Comment: GAPIT p-value significance threshold
by
ginellegrenier
• 0
Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot
by
jkim
▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
Comment: ScRNA data question
by
bk11
★ 2.3k
Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis?
by
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• 0
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Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
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141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
Comment: Figures are disappeared from html report of SnpEff
by
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161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
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161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff
by
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▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
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I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
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so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
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161k
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