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8
votes
12
replies
506
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse r
21 hours ago by Assa Yeroslaviz ★ 1.9k
0
votes
1
reply
161
views
Can I count UMI-barcode combination without mapping?
HyDrop protein UMI UMI-Tools
updated 3 days ago by 142k • written 3 days ago by ★ 1.9k
1
vote
2
replies
289
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat Violin-Plot ggplot2 patchwork
23 days ago by Assa Yeroslaviz ★ 1.9k
5
votes
12
replies
600
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 2 days ago by 19k • written 24 days ago by ★ 1.9k
0
votes
3
replies
246
views
trying to count a pattern in my fastq file using bbduk
java bbduk bbmap fastq
updated 24 days ago by 142k • written 24 days ago by ★ 1.9k
0
votes
3
replies
535
views
why renaming Idents in Seurat object doesn't work?
Seurat RenameIdents R
4 weeks ago by Assa Yeroslaviz ★ 1.9k
1
vote
9
replies
657
views
Can index hopping lead to more reads in samples?
index-hopping NovoSeq illumina NGS Seqeucning
8 weeks ago by Assa Yeroslaviz ★ 1.9k
0
votes
0
replies
267
views
What does it means, when 2-direction perturbed pathways are identified in the gage enrichment analysis?
r pathway go-enrichment gage
8 weeks ago by Assa Yeroslaviz ★ 1.9k
0
votes
2
replies
328
views
annotating single-cell clusters from gene lists
annotation FindAllMarkers Seurat cell-type
updated 3 months ago by 44k • written 3 months ago by ★ 1.9k
0
votes
0
replies
159
views
Correlating Chip-Seq and proteimics results
chip-seq correlations proteomics
4 months ago by Assa Yeroslaviz ★ 1.9k
0
votes
0
replies
220
views
Understanding Homer output for makeTagDirectory
chip-seq peaks homer makeTagDirectory
4 months ago by Assa Yeroslaviz ★ 1.9k
3
votes
4
replies
625
views
split sequences into their codons in a table
R fasta codon-table
4 months ago by Assa Yeroslaviz ★ 1.9k
0
votes
0
replies
180
views
cross-correlation peak at position 0 when calculating ChIp-Seq
cross-correlation peak chip-seq phantompeak ChIPseeker
4 months ago by Assa Yeroslaviz ★ 1.9k
1
vote
1
reply
328
views
Annotating peak using Chipseeker for non-model organism
GenomicFeatures chipseq chipseeker annoDB TxDb
updated 4 months ago by 13k • written 4 months ago by ★ 1.9k
1
vote
8
replies
1.6k
views
counts of cite-seq-count vs. cellrenager varies tremendously
citeseq-count cellranger cite-seq scRNA-seq
updated 5 months ago by 83k • written 10 months ago by ★ 1.9k
0
votes
0
replies
268
views
extracting Uniprot IDs for Kegg pathways
mapping uniprot R kegg clusterprofiler
5 months ago by Assa Yeroslaviz ★ 1.9k
1
vote
4
replies
637
views
Plotting gene Expression per pathway
GO-enrichment gene-expression R ggplot RNA-seq
7 months ago by Assa Yeroslaviz ★ 1.9k
3
votes
6
replies
916
views
summarize consecutive columns over a data frame
tidyverse r offtopic
updated 8 months ago by 44k • written 8 months ago by ★ 1.9k
1
vote
3
replies
852
views
trajectory-like graph for a data frame
trajectory rna-seq tidyverse r velocity
updated 8 months ago by ★ 17k • written 8 months ago by ★ 1.9k
0
votes
4
replies
619
views
WGS sequencing data based proteomics analysis
workflow UniProt proteomics WGS RNA-Seq
updated 10 months ago by ★ 1.1k • written 10 months ago by ★ 1.9k
0
votes
2
replies
419
views
Checking significance in trend of time-series analysis for count data
glm RNA-Seq time-series
11 months ago by Assa Yeroslaviz ★ 1.9k
1
vote
5
replies
913
views
annotating single-cell cluster from Drosophila melanogaster using SingleR?
SingleR celldex cell-type-annotations scRNA
updated 11 months ago by ★ 1.6k • written 11 months ago by ★ 1.9k
2
votes
2
replies
963
views
6 follow
Why runing scDblFinder before and after removing low QC cells gives different results
singleCellExperiment scDblFinder SMART-Seq
updated 6 months ago by ▴ 210 • written 11 months ago by ★ 1.9k
0
votes
1
reply
1.3k
views
what is the difference between FindVariableFeatures and FindAllMarkers?
Seurat single-cell FindVariableFeatures FindAllMarkers RNA-Seq
updated 12 months ago by 13k • written 12 months ago by ★ 1.9k
5
votes
2
replies
682
views
ERCC normalization within DESeq2
normalization ERCC size.factors DESeq2
updated 13 months ago by 83k • written 13 months ago by ★ 1.9k
8
votes
5
replies
2.3k
views
DESeq2 model matrix not full rank
full-rank model-matrix deseq2
updated 13 months ago by 142k • written 2.9 years ago by ★ 1.9k
1
vote
1
reply
485
views
Can I add labels to (some) cells in a plotColData from scater?
single-cell-experiment plotColData scater
13 months ago by Assa Yeroslaviz ★ 1.9k
0
votes
0
replies
396
views
How to normalise ChIP-Seq samples using deeptools
bamCoverage deepTools
updated 11 months ago by 44k • written 14 months ago by ★ 1.9k
10
votes
17
replies
3.4k
views
How do one analyze data from SMART-Seq stranded kit (v4)?
single-cell smart-seq
updated 14 months ago by ★ 6.1k • written 15 months ago by ★ 1.9k
0
votes
0
replies
426
views
bamComparing ChIp-Seq samples with strange coverage between chipped and Input
normalization bamCompare deepTools
updated 11 months ago by 44k • written 15 months ago by ★ 1.9k
3
votes
4
replies
2.7k
views
STAR aligner can't map too short reads
ribo-seq star
updated 16 months ago by 19k • written 16 months ago by ★ 1.9k
4
votes
3
replies
967
views
How to calculate the offset for a riboseq experiment
sequencing p-site riboseq offset
updated 18 months ago by ▴ 360 • written 18 months ago by ★ 1.9k
5
votes
4
replies
1.3k
views
How to interpret the nine-square plot from mageckFlute
mageck mageckFlute squareView scatterplot
18 months ago by Assa Yeroslaviz ★ 1.9k
1
vote
5
replies
860
views
Need help understanding GEO data structure
Run-Selector GEO gene-expression-omnibus
updated 18 months ago by 142k • written 18 months ago by ★ 1.9k
4
votes
2
replies
609
views
How to extract min and max values of a gene from different columns
group_by tibble tidyverse
updated 19 months ago by 14k • written 19 months ago by ★ 1.9k
3
votes
2
replies
574
views
expanding a table by duplicating rows of a specific pattern
tidyyverse dplyr R data.frame
20 months ago by Assa Yeroslaviz ★ 1.9k
2
votes
3
replies
639
views
Identifying binding sequences of a specific protein to its target
transcription-factor-binding-site gene-regulation transcription-factor
21 months ago by Assa Yeroslaviz ★ 1.9k
0
votes
2
replies
743
views
Ca you help me understand the Nanopore fastqc results?
pycoQC long-read-seq nanopore fastqc
2.1 years ago by Assa Yeroslaviz ★ 1.9k
8
votes
7
replies
2.9k
views
Help me understand the Nanopore fastqc results
long-read-seq nanopore fastqc
updated 2.1 years ago by 100k • written 2.1 years ago by ★ 1.9k
15
votes
11
replies
8.9k
views
6 follow
filter out fasta File by pattern
pattern fasta awk sed regexp
updated 2.1 years ago by 21k • written 9.2 years ago by ★ 1.9k
0
votes
0
replies
353
views
pQTL analysis
plink GWAS pQTL linkage-disequilibrium
2.2 years ago by Assa Yeroslaviz ★ 1.9k
0
votes
0
replies
430
views
Understanding DEXSeq results
dexseq normalization counts
2.3 years ago by Assa Yeroslaviz ★ 1.9k
3
votes
1
reply
513
views
Basic understanding of Hi-C and interacion (contact-) maps
TADs interactions contact-maps AB-compartments HiC
updated 2.3 years ago by 83k • written 2.3 years ago by ★ 1.9k
1
vote
1
reply
821
views
Hoe do you do differential Splicing using edgeR command diffSpliceDGE?
differential-splicing edger diffSpliceDGE
updated 2.3 years ago by ▴ 120 • written 2.3 years ago by ★ 1.9k
5
votes
5
replies
5.3k
views
How do I compare reads between two bam file?
samtools reads bam compare
updated 2.6 years ago by 162k • written 2.6 years ago by ★ 1.9k
0
votes
0
replies
481
views
comparing distinct peaks from riboseq profiling results
ribosomal-profiling ribo-seq peaks
3.1 years ago by Assa Yeroslaviz ★ 1.9k
0
votes
0
replies
858
views
adjust size of png images in a rasterGrob object
rasterGrob PNG Rmarkdown layout
3.2 years ago by Assa Yeroslaviz ★ 1.9k
2
votes
1
reply
781
views
Mapping after WGS show a parabel form
WGS mapping SNP CNV
updated 3.1 years ago by ▴ 10 • written 3.2 years ago by ★ 1.9k
0
votes
2
replies
837
views
Modifying an annotation files after transgene insertion
transgene insertion gtf annotation
3.2 years ago by Assa Yeroslaviz ★ 1.9k
1
vote
2
replies
1.4k
views
how many reads are necessary for Ribo-Seq analysis
riboseq ribosome profiling ribo-seq
updated 3.3 years ago by • 0 • written 5.1 years ago by ★ 1.9k
202 results • Page 1 of 5
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