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1
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7
replies
722
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Before doing pseudobulk, should we get rid of genes that are only expressed in a small number of cells?
DESeq2 scRNAseq Pseudobulk
10 weeks ago by mropri ▴ 150
3
votes
5
replies
479
views
How to account for total number of cells when aggregating for pseudobulk?
Pseudobulk
updated 10 weeks ago by 84k • written 10 weeks ago by ▴ 150
2
votes
2
replies
779
views
Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment? (Already checke…
DESeq2
11 weeks ago by mropri ▴ 150
0
votes
3
replies
550
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
4 months ago by mropri ▴ 150
0
votes
2
replies
423
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
4 months ago by mropri ▴ 150
0
votes
4
replies
528
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics scRNA-seq proliferation
5 weeks ago by mropri ▴ 150
0
votes
2
replies
2.4k
views
ROSE Algorithm for Ranking Super Enhancers
ChIP-Seq
updated 7 months ago by 44k • written 4.2 years ago by ▴ 150
0
votes
2
replies
966
views
Is it necessary to integrate again samples when subclustering
scRNA-seq integration Single-cell
updated 8 months ago by 44k • written 8 months ago by ▴ 150
0
votes
0
replies
257
views
Running MultiK on one single cell sample, is it that memory intensive
MultiK Single-Cell
updated 8 months ago by 44k • written 8 months ago by ▴ 150
0
votes
2
replies
901
views
Single Cell RNA-seq analysis one by one vs all together
scRNA-seq single-cell
8 months ago by mropri ▴ 150
0
votes
0
replies
320
views
Check if BAMboozle anonymized bam files
BAMboozle
14 months ago by mropri ▴ 150
0
votes
8
replies
1.1k
views
BAMboozle
BAMboozle
16 months ago by mropri ▴ 150
0
votes
3
replies
949
views
Picard ribosome intervals list
Picard
16 months ago by mropri ▴ 150
0
votes
1
reply
1.5k
views
Cannot install limma
bioconductor limma
updated 17 months ago by ▴ 610 • written 17 months ago by ▴ 150
2
votes
6
replies
1.4k
views
Older version of SVA (Surrogate Variable Analysis) in R using Bioconductor?
Bioconductor SVA
17 months ago by mropri ▴ 150
3
votes
2
replies
582
views
Power analysis for patient samples
RNA-seq
18 months ago by mropri ▴ 150
6
votes
6
replies
1.4k
views
Use single cell sequencing bam file to tell if a patient has a mutation
Cell Single RNA sequencing
19 months ago by mropri ▴ 150
0
votes
6
replies
915
views
GO analysis where I can set by own set of genes to search against
Analysis GO
23 months ago by mropri ▴ 150
2
votes
5
replies
1.4k
views
Sabre demultiplexer
demultiplexing Sabre RNA-seq
updated 2.0 years ago by 145k • written 2.3 years ago by ▴ 150
0
votes
0
replies
475
views
Corr.test method
Correlation corr.test r
2.1 years ago by mropri ▴ 150
1
vote
4
replies
2.7k
views
Creating a script to run STAR alignment on multiple fastq files
RNA-seq STAR Alignment
2.3 years ago by mropri ▴ 150
0
votes
14
replies
2.3k
views
Corrplot heatmap crunched up and unreadable
Corrplot heatmap
2.3 years ago by mropri ▴ 150
2
votes
2
replies
767
views
Create a heatmap of only significant correlations
Correlation Protein expression heatmap
updated 2.3 years ago by 44k • written 2.3 years ago by ▴ 150
3
votes
2
replies
724
views
Filter Protein Expression Data
Filtering Proteomics
updated 2.3 years ago by 44k • written 2.3 years ago by ▴ 150
2
votes
3
replies
789
views
Impute protein expression matrix
Protein Impute Expression
updated 2.3 years ago by ▴ 910 • written 2.3 years ago by ▴ 150
5
votes
13
replies
3.8k
views
How to regress out age and sex using limma removeBatchEffect
removeBatchEffect expression data Limma
updated 14 months ago by ★ 7.3k • written 2.3 years ago by ▴ 150
1
vote
2
replies
1.3k
views
How to perform VST on my filtered counts data
RNA-seq transformation VST
updated 2.4 years ago by 14k • written 2.4 years ago by ▴ 150
0
votes
0
replies
489
views
Identical peak coverage in IP bam file and Input bam file
ChIP-Seq
3.0 years ago by mropri ▴ 150
0
votes
1
reply
1.0k
views
ChIP QC
QC ChIP
updated 3.3 years ago by 44k • written 3.3 years ago by ▴ 150
2
votes
4
replies
2.2k
views
bedGraphToBigWig
Seq ChIP
updated 3.4 years ago by ★ 17k • written 3.4 years ago by ▴ 150
0
votes
12
replies
4.9k
views
DiffBind error when calling dba.count
ChIP-Seq
updated 3.6 years ago by • 0 • written 4.3 years ago by ▴ 150
5
votes
9
replies
3.1k
views
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
RNA-Seq R
updated 3.8 years ago by 44k • written 3.8 years ago by ▴ 150
12
votes
16
replies
1.8k
views
Error: SortDetails.cpp, 1111: Unable to create FILE* for temp file: No space left on device. Out of memory.
ChIP-Seq
updated 3.8 years ago by 35k • written 3.8 years ago by ▴ 150
6
votes
20
replies
2.4k
views
Use bedtools intersect to see how much coverage you had of a specific coordinate
ChIP-Seq
updated 3.8 years ago by 35k • written 3.8 years ago by ▴ 150
1
vote
3
replies
1.8k
views
Collapse two or thee bed files into one bed file using bedtools merge
ChIP-Seq
updated 3.8 years ago by 84k • written 3.8 years ago by ▴ 150
6
votes
7
replies
1.2k
views
Compare Super Enhancers in normal vs breast cancer cells
ChIP-Seq
updated 3.8 years ago by ★ 17k • written 3.8 years ago by ▴ 150
3
votes
5
replies
1.4k
views
Error: No Space left on device
rna-seq
updated 3.9 years ago by 145k • written 3.9 years ago by ▴ 150
0
votes
3
replies
938
views
Differential Gene Expression Using Deseq2
RNA-Seq
updated 4.1 years ago by ★ 1.5k • written 4.1 years ago by ▴ 150
2
votes
3
replies
1.3k
views
Filtering lncRNAs from total RNA
RNA-Seq
4.1 years ago by mropri ▴ 150
1
vote
4
replies
2.5k
views
Sicer peak calling
ChIP-Seq
updated 4.2 years ago by ★ 17k • written 4.2 years ago by ▴ 150
1
vote
4
replies
734
views
Copy column to another column in the same file
ChIP-Seq
updated 4.2 years ago by ★ 17k • written 4.2 years ago by ▴ 150
0
votes
3
replies
1.2k
views
Using genome tools to convert bed files to gff3 files
ChIP-Seq
updated 4.2 years ago by 8.7k • written 4.2 years ago by ▴ 150
0
votes
8
replies
2.1k
views
ROSE Algorithm: index out of range
ChIP-Seq
updated 11 months ago by 44k • written 4.2 years ago by ▴ 150
0
votes
4
replies
2.0k
views
ROSE Algorithm: Error when importing upper and join from string
ChIP-Seq
updated 4.2 years ago by ★ 17k • written 4.2 years ago by ▴ 150
0
votes
6
replies
2.2k
views
ChIP seq: Trying to use ChIPQC to measure quality of reads
ChIP-Seq
4.3 years ago by mropri ▴ 150
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