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0
votes
3
replies
413
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why renaming Idents in Seurat object doesn't work?
Seurat RenameIdents R
6 days ago by Assa Yeroslaviz ★ 1.8k
1
vote
9
replies
574
views
Can index hopping lead to more reads in samples?
index-hopping NovoSeq illumina NGS Seqeucning
4 weeks ago by Assa Yeroslaviz ★ 1.8k
0
votes
0
replies
257
views
What does it means, when 2-direction perturbed pathways are identified in the gage enrichment analysis?
r pathway go-enrichment gage
4 weeks ago by Assa Yeroslaviz ★ 1.8k
0
votes
2
replies
297
views
annotating single-cell clusters from gene lists
annotation FindAllMarkers Seurat cell-type
updated 10 weeks ago by 43k • written 10 weeks ago by ★ 1.8k
0
votes
0
replies
142
views
Correlating Chip-Seq and proteimics results
chip-seq correlations proteomics
3 months ago by Assa Yeroslaviz ★ 1.8k
0
votes
0
replies
195
views
Understanding Homer output for makeTagDirectory
chip-seq peaks homer makeTagDirectory
3 months ago by Assa Yeroslaviz ★ 1.8k
3
votes
4
replies
579
views
split sequences into their codons in a table
R fasta codon-table
3 months ago by Assa Yeroslaviz ★ 1.8k
0
votes
0
replies
162
views
cross-correlation peak at position 0 when calculating ChIp-Seq
cross-correlation peak chip-seq phantompeak ChIPseeker
3 months ago by Assa Yeroslaviz ★ 1.8k
1
vote
1
reply
287
views
Annotating peak using Chipseeker for non-model organism
GenomicFeatures chipseq chipseeker annoDB TxDb
updated 3 months ago by 13k • written 3 months ago by ★ 1.8k
1
vote
8
replies
1.5k
views
counts of cite-seq-count vs. cellrenager varies tremendously
citeseq-count cellranger cite-seq scRNA-seq
updated 4 months ago by 82k • written 9 months ago by ★ 1.8k
0
votes
0
replies
251
views
extracting Uniprot IDs for Kegg pathways
mapping uniprot R kegg clusterprofiler
5 months ago by Assa Yeroslaviz ★ 1.8k
1
vote
4
replies
603
views
Plotting gene Expression per pathway
GO-enrichment gene-expression R ggplot RNA-seq
6 months ago by Assa Yeroslaviz ★ 1.8k
3
votes
6
replies
876
views
summarize consecutive columns over a data frame
tidyverse r offtopic
updated 7 months ago by 43k • written 7 months ago by ★ 1.8k
1
vote
3
replies
819
views
trajectory-like graph for a data frame
trajectory rna-seq tidyverse r velocity
updated 7 months ago by ★ 16k • written 8 months ago by ★ 1.8k
0
votes
4
replies
601
views
WGS sequencing data based proteomics analysis
workflow UniProt proteomics WGS RNA-Seq
updated 9 months ago by ★ 1.1k • written 9 months ago by ★ 1.8k
0
votes
2
replies
409
views
Checking significance in trend of time-series analysis for count data
glm RNA-Seq time-series
10 months ago by Assa Yeroslaviz ★ 1.8k
1
vote
5
replies
876
views
annotating single-cell cluster from Drosophila melanogaster using SingleR?
SingleR celldex cell-type-annotations scRNA
updated 10 months ago by ★ 1.6k • written 10 months ago by ★ 1.8k
2
votes
2
replies
903
views
6 follow
Why runing scDblFinder before and after removing low QC cells gives different results
singleCellExperiment scDblFinder SMART-Seq
updated 5 months ago by ▴ 210 • written 10 months ago by ★ 1.8k
0
votes
1
reply
1.2k
views
what is the difference between FindVariableFeatures and FindAllMarkers?
Seurat single-cell FindVariableFeatures FindAllMarkers RNA-Seq
updated 11 months ago by 13k • written 11 months ago by ★ 1.8k
5
votes
2
replies
646
views
ERCC normalization within DESeq2
normalization ERCC size.factors DESeq2
updated 12 months ago by 82k • written 12 months ago by ★ 1.8k
8
votes
5
replies
2.3k
views
DESeq2 model matrix not full rank
full-rank model-matrix deseq2
updated 12 months ago by 142k • written 2.9 years ago by ★ 1.8k
1
vote
1
reply
473
views
Can I add labels to (some) cells in a plotColData from scater?
single-cell-experiment plotColData scater
12 months ago by Assa Yeroslaviz ★ 1.8k
0
votes
0
replies
387
views
How to normalise ChIP-Seq samples using deeptools
bamCoverage deepTools
updated 10 months ago by 43k • written 13 months ago by ★ 1.8k
10
votes
17
replies
3.2k
views
How do one analyze data from SMART-Seq stranded kit (v4)?
single-cell smart-seq
updated 14 months ago by ★ 6.0k • written 14 months ago by ★ 1.8k
0
votes
0
replies
410
views
bamComparing ChIp-Seq samples with strange coverage between chipped and Input
normalization bamCompare deepTools
updated 10 months ago by 43k • written 14 months ago by ★ 1.8k
3
votes
4
replies
2.6k
views
STAR aligner can't map too short reads
ribo-seq star
updated 15 months ago by 19k • written 15 months ago by ★ 1.8k
4
votes
3
replies
929
views
How to calculate the offset for a riboseq experiment
sequencing p-site riboseq offset
updated 17 months ago by ▴ 360 • written 17 months ago by ★ 1.8k
5
votes
4
replies
1.2k
views
How to interpret the nine-square plot from mageckFlute
mageck mageckFlute squareView scatterplot
17 months ago by Assa Yeroslaviz ★ 1.8k
1
vote
5
replies
825
views
Need help understanding GEO data structure
Run-Selector GEO gene-expression-omnibus
updated 18 months ago by 142k • written 18 months ago by ★ 1.8k
4
votes
2
replies
589
views
How to extract min and max values of a gene from different columns
group_by tibble tidyverse
updated 18 months ago by 14k • written 18 months ago by ★ 1.8k
3
votes
2
replies
558
views
expanding a table by duplicating rows of a specific pattern
tidyyverse dplyr R data.frame
19 months ago by Assa Yeroslaviz ★ 1.8k
2
votes
3
replies
622
views
Identifying binding sequences of a specific protein to its target
transcription-factor-binding-site gene-regulation transcription-factor
20 months ago by Assa Yeroslaviz ★ 1.8k
0
votes
2
replies
704
views
Ca you help me understand the Nanopore fastqc results?
pycoQC long-read-seq nanopore fastqc
24 months ago by Assa Yeroslaviz ★ 1.8k
8
votes
7
replies
2.7k
views
Help me understand the Nanopore fastqc results
long-read-seq nanopore fastqc
updated 2.0 years ago by 100k • written 2.0 years ago by ★ 1.8k
15
votes
11
replies
8.8k
views
6 follow
filter out fasta File by pattern
pattern fasta awk sed regexp
updated 24 months ago by 21k • written 9.2 years ago by ★ 1.8k
0
votes
0
replies
346
views
pQTL analysis
plink GWAS pQTL linkage-disequilibrium
2.2 years ago by Assa Yeroslaviz ★ 1.8k
0
votes
0
replies
417
views
Understanding DEXSeq results
dexseq normalization counts
2.2 years ago by Assa Yeroslaviz ★ 1.8k
3
votes
1
reply
502
views
Basic understanding of Hi-C and interacion (contact-) maps
TADs interactions contact-maps AB-compartments HiC
updated 2.3 years ago by 82k • written 2.3 years ago by ★ 1.8k
1
vote
1
reply
776
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 ★ 1.8k
5
votes
5
replies
5.1k
views
How do I compare reads between two bam file?
samtools reads bam compare
updated 2.6 years ago by 161k • written 2.6 years ago by ★ 1.8k
0
votes
0
replies
476
views
comparing distinct peaks from riboseq profiling results
ribosomal-profiling ribo-seq peaks
3.0 years ago by Assa Yeroslaviz ★ 1.8k
0
votes
0
replies
845
views
adjust size of png images in a rasterGrob object
rasterGrob PNG Rmarkdown layout
3.1 years ago by Assa Yeroslaviz ★ 1.8k
2
votes
1
reply
772
views
Mapping after WGS show a parabel form
WGS mapping SNP CNV
updated 3.1 years ago by ▴ 10 • written 3.1 years ago by ★ 1.8k
0
votes
2
replies
814
views
Modifying an annotation files after transgene insertion
transgene insertion gtf annotation
3.2 years ago by Assa Yeroslaviz ★ 1.8k
1
vote
2
replies
1.3k
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 ★ 1.8k
1
vote
0
replies
741
views
How to do a normalization onto mtRNAs
mtRNA normalization rna-seq
updated 3.4 years ago by 20 • written 3.5 years ago by ★ 1.8k
3
votes
9
replies
953
views
How can I annotate multiple blast results?
blast annotation
updated 3.4 years ago by 142k • written 3.4 years ago by ★ 1.8k
4
votes
4
replies
1.8k
views
How to annotate a bam file?
bam annotations
3.5 years ago by Assa Yeroslaviz ★ 1.8k
1
vote
2
replies
1.9k
views
ggplot2 scater plot with three grouping parameters
ggplot2 PCA aes
3.5 years ago by Assa Yeroslaviz ★ 1.8k
1
vote
6
replies
1.8k
views
bcftools mpileup create an empty output file
bcftools mpileup samtools bwa bam
3.5 years ago by Assa Yeroslaviz ★ 1.8k
197 results • Page 1 of 4
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