Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
Showing : questions
1
vote
9
replies
400
views
How do I integrate public annotated data onto my data set?
SelectIntegrationFeatures IntegrateData Seurat tabula-muris
updated 12 days ago by 5.9k • written 12 days ago by ★ 1.9k
3
votes
1
reply
207
views
color specific genes in VariableFeaturePlot
ggplot2 VariableFeaturePlot Seurat
updated 21 days ago by 5.9k • written 21 days ago by ★ 1.9k
0
votes
0
replies
229
views
mageck mle design matrix
crispr mageck-mle design-matrix pooled-screen
4 weeks ago by Assa Yeroslaviz ★ 1.9k
1
vote
2
replies
555
views
After subsetting a seurat object number of variable features is wrong.
FindVariableFeatures seurat subset
updated 4 weeks ago by 44k • written 3 months ago by ★ 1.9k
0
votes
0
replies
121
views
Using RunAzimuth with pbmcref on mouse data
mouse scRNA-Seq Suerat Azimuth
6 weeks ago by Assa Yeroslaviz ★ 1.9k
1
vote
10
replies
770
views
Does mageck-vispr calculate differently than mageck?
mageck mageck-vispr pooled-screen cripsr
5 weeks ago by Assa Yeroslaviz ★ 1.9k
0
votes
6
replies
626
views
installing ArchR on a mac
R ArchR
7 weeks ago by Assa Yeroslaviz ★ 1.9k
4
votes
3
replies
446
views
remove the letter a from a biplot in ggplot
legend biplot ggplot guides
updated 12 weeks ago by ▴ 280 • written 12 weeks ago by ★ 1.9k
4
votes
4
replies
634
views
How to understand differences in duplication rates between picard MarkDuplicates and fastp
duplication-rate rna-seq fastp picard
3 months ago by Assa Yeroslaviz ★ 1.9k
4
votes
2
replies
677
views
Understanding Differing results between STAR and kallisto
quantification STAR kallisto RNA-Seq
updated 5 months ago by ★ 1.3k • written 5 months ago by ★ 1.9k
1
vote
4
replies
646
views
Volcano plot with different font size for gene labels
rna-seq enhancedVolcano volcano-plot
updated 5 months ago by ★ 1.8k • written 5 months ago by ★ 1.9k
1
vote
5
replies
2.2k
views
Error in converting bed file to interval using Picard
WES exome BedToIntervalList picard agilent
updated 5 months ago by 44k • written 5.0 years ago by ★ 1.9k
9
votes
13
replies
1.0k
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse r
updated 6 months ago by ▴ 210 • written 6 months ago by ★ 1.9k
0
votes
1
reply
343
views
Can I count UMI-barcode combination without mapping?
HyDrop protein UMI UMI-Tools
updated 6 months ago by 147k • written 6 months ago by ★ 1.9k
1
vote
2
replies
1.2k
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat Violin-Plot ggplot2 patchwork
6 months ago by Assa Yeroslaviz ★ 1.9k
5
votes
12
replies
1.2k
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 6 months ago by 20k • written 6 months ago by ★ 1.9k
0
votes
3
replies
402
views
trying to count a pattern in my fastq file using bbduk
java bbduk bbmap fastq
updated 6 months ago by 147k • written 6 months ago by ★ 1.9k
0
votes
3
replies
1.2k
views
why renaming Idents in Seurat object doesn't work?
Seurat RenameIdents R
7 months ago by Assa Yeroslaviz ★ 1.9k
1
vote
9
replies
1.2k
views
Can index hopping lead to more reads in samples?
index-hopping NovoSeq illumina NGS Seqeucning
8 months ago by Assa Yeroslaviz ★ 1.9k
0
votes
0
replies
355
views
What does it means, when 2-direction perturbed pathways are identified in the gage enrichment analysis?
r pathway go-enrichment gage
8 months ago by Assa Yeroslaviz ★ 1.9k
0
votes
2
replies
468
views
annotating single-cell clusters from gene lists
annotation FindAllMarkers Seurat cell-type
updated 9 months ago by 44k • written 9 months ago by ★ 1.9k
0
votes
0
replies
226
views
Correlating Chip-Seq and proteimics results
chip-seq correlations proteomics
10 months ago by Assa Yeroslaviz ★ 1.9k
0
votes
0
replies
355
views
Understanding Homer output for makeTagDirectory
chip-seq peaks homer makeTagDirectory
10 months ago by Assa Yeroslaviz ★ 1.9k
3
votes
4
replies
781
views
split sequences into their codons in a table
R fasta codon-table
10 months ago by Assa Yeroslaviz ★ 1.9k
0
votes
0
replies
251
views
cross-correlation peak at position 0 when calculating ChIp-Seq
cross-correlation peak chip-seq phantompeak ChIPseeker
10 months ago by Assa Yeroslaviz ★ 1.9k
1
vote
1
reply
466
views
Annotating peak using Chipseeker for non-model organism
GenomicFeatures chipseq chipseeker annoDB TxDb
updated 10 months ago by 13k • written 10 months ago by ★ 1.9k
1
vote
8
replies
2.0k
views
counts of cite-seq-count vs. cellrenager varies tremendously
citeseq-count cellranger cite-seq scRNA-seq
updated 11 months ago by 85k • written 16 months ago by ★ 1.9k
0
votes
0
replies
371
views
extracting Uniprot IDs for Kegg pathways
mapping uniprot R kegg clusterprofiler
12 months ago by Assa Yeroslaviz ★ 1.9k
1
vote
4
replies
882
views
Plotting gene Expression per pathway
GO-enrichment gene-expression R ggplot RNA-seq
13 months ago by Assa Yeroslaviz ★ 1.9k
3
votes
6
replies
1.2k
views
summarize consecutive columns over a data frame
tidyverse r offtopic
updated 14 months ago by 44k • written 14 months ago by ★ 1.9k
1
vote
3
replies
1.0k
views
trajectory-like graph for a data frame
trajectory rna-seq tidyverse r velocity
updated 14 months ago by ★ 18k • written 15 months ago by ★ 1.9k
0
votes
4
replies
789
views
WGS sequencing data based proteomics analysis
workflow UniProt proteomics WGS RNA-Seq
updated 16 months ago by ★ 1.3k • written 16 months ago by ★ 1.9k
0
votes
2
replies
529
views
Checking significance in trend of time-series analysis for count data
glm RNA-Seq time-series
17 months ago by Assa Yeroslaviz ★ 1.9k
1
vote
5
replies
1.2k
views
annotating single-cell cluster from Drosophila melanogaster using SingleR?
SingleR celldex cell-type-annotations scRNA
updated 17 months ago by ★ 1.6k • written 17 months ago by ★ 1.9k
2
votes
2
replies
1.3k
views
6 follow
Why runing scDblFinder before and after removing low QC cells gives different results
singleCellExperiment scDblFinder SMART-Seq
updated 12 months ago by ▴ 230 • written 17 months ago by ★ 1.9k
0
votes
1
reply
1.7k
views
what is the difference between FindVariableFeatures and FindAllMarkers?
Seurat single-cell FindVariableFeatures FindAllMarkers RNA-Seq
updated 18 months ago by 13k • written 18 months ago by ★ 1.9k
5
votes
2
replies
878
views
ERCC normalization within DESeq2
normalization ERCC size.factors DESeq2
updated 19 months ago by 85k • written 19 months ago by ★ 1.9k
9
votes
5
replies
2.7k
views
DESeq2 model matrix not full rank
full-rank model-matrix deseq2
updated 19 months ago by 147k • written 3.4 years ago by ★ 1.9k
1
vote
1
reply
582
views
Can I add labels to (some) cells in a plotColData from scater?
single-cell-experiment plotColData scater
19 months ago by Assa Yeroslaviz ★ 1.9k
0
votes
0
replies
455
views
How to normalise ChIP-Seq samples using deeptools
bamCoverage deepTools
updated 17 months ago by 44k • written 20 months ago by ★ 1.9k
10
votes
17
replies
4.4k
views
How do one analyze data from SMART-Seq stranded kit (v4)?
single-cell smart-seq
updated 21 months ago by ★ 6.9k • written 21 months ago by ★ 1.9k
0
votes
0
replies
505
views
bamComparing ChIp-Seq samples with strange coverage between chipped and Input
normalization bamCompare deepTools
updated 17 months ago by 44k • written 21 months ago by ★ 1.9k
4
votes
4
replies
4.2k
views
STAR aligner can't map too short reads
ribo-seq star
updated 22 months ago by 20k • written 22 months ago by ★ 1.9k
4
votes
3
replies
1.2k
views
How to calculate the offset for a riboseq experiment
sequencing p-site riboseq offset
updated 24 months ago by ▴ 410 • written 2.0 years ago by ★ 1.9k
5
votes
4
replies
1.6k
views
How to interpret the nine-square plot from mageckFlute
mageck mageckFlute squareView scatterplot
24 months ago by Assa Yeroslaviz ★ 1.9k
1
vote
5
replies
1.1k
views
Need help understanding GEO data structure
Run-Selector GEO gene-expression-omnibus
updated 2.1 years ago by 147k • written 2.1 years ago by ★ 1.9k
4
votes
2
replies
740
views
How to extract min and max values of a gene from different columns
group_by tibble tidyverse
updated 2.1 years ago by 15k • written 2.1 years ago by ★ 1.9k
3
votes
2
replies
677
views
expanding a table by duplicating rows of a specific pattern
tidyyverse dplyr R data.frame
2.2 years ago by Assa Yeroslaviz ★ 1.9k
2
votes
3
replies
750
views
Identifying binding sequences of a specific protein to its target
transcription-factor-binding-site gene-regulation transcription-factor
2.3 years ago by Assa Yeroslaviz ★ 1.9k
0
votes
2
replies
848
views
Ca you help me understand the Nanopore fastqc results?
pycoQC long-read-seq nanopore fastqc
2.6 years ago by Assa Yeroslaviz ★ 1.9k
213 results • Page 1 of 5
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6