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0
votes
6
replies
923
views
Estimating hetero/homogeneity of scRNAseq clusters
scRNA-seq R
updated 3.3 years ago by 20 • written 3.4 years ago by ▴ 200
5
votes
2
replies
2.8k
views
What are the differences between the Seurat v3 clustering algorithms?
scRNA-seq Seurat R
3.5 years ago by jrleary ▴ 200
4
votes
1
reply
5.3k
views
Can I manually add nCount_RNA & nFeature_RNA to a converted Seurat object?
scRNA-seq Seurat R
3.5 years ago by jrleary ▴ 200
0
votes
4
replies
1.7k
views
How should I extract mutated genes from a VCF file?
WES exome gatk
3.5 years ago by jrleary ▴ 200
2
votes
3
replies
2.8k
views
How much RAM / how many CPUs should I allocate for Mutect2?
WES
updated 3.5 years ago by ★ 3.4k • written 3.5 years ago by ▴ 200
2
votes
11
replies
1.7k
views
Picard CollectSequencingArtifactMetrics error
picard WES
3.5 years ago by jrleary ▴ 200
3
votes
2
replies
1.4k
views
Coloring single cell dimension-reduced plots in R, which palettes can handle high n?
R ggplot2
3.6 years ago by jrleary ▴ 200
1
vote
2
replies
657
views
Where to find reference transcriptome for firefly?
scRNA-seq cellranger alignment transcriptome
updated 3.6 years ago by 136k • written 3.6 years ago by ▴ 200
3
votes
3
replies
1.2k
views
Salmon only processes human reads from PDX data
salmon RNA-Seq alignment software error
updated 3.6 years ago by ▴ 50 • written 3.9 years ago by ▴ 200
2
votes
3
replies
1.8k
views
Papers on Paired Single Cell and Bulk RNAseq
RNA-Seq scRNA-seq
updated 3.7 years ago by ▴ 10 • written 3.7 years ago by ▴ 200
12
votes
14
replies
3.0k
views
Identifying tumor cells in single cell RNAseq data
cancer scRNAseq R
updated 3.8 years ago by ★ 16k • written 3.8 years ago by ▴ 200
11
votes
9
replies
2.1k
views
Recommendations for Whole Genome Sequencing Workflow
WGS genome Assembly
updated 3.8 years ago by ▴ 960 • written 3.8 years ago by ▴ 200
3
votes
2
replies
2.6k
views
Any recommendations for copy number variation (CNV) packages for scRNA-seq?
single cell scRNAseq CNV R
updated 3.8 years ago by ★ 16k • written 3.8 years ago by ▴ 200
0
votes
1
reply
715
views
Should cells be rows or columns when dimension reducing scRNAseq data?
scRNAseq single cell analysis
3.9 years ago by jrleary ▴ 200
3
votes
9
replies
3.1k
views
Is it appropriate to use counts = counts + 1 when using DESeq2 on scRNAseq data?
sc-rnaseq differential expression
updated 4.0 years ago by 13k • written 4.0 years ago by ▴ 200
9
votes
8
replies
6.5k
views
Should I Run Clustering on PCA or t-SNE Components?
sc-rnaseq clustering
updated 4.0 years ago by ★ 25k • written 4.0 years ago by ▴ 200
0
votes
5
replies
1.1k
views
C++ versus Python for dimension reduction / clustering speed?
cpp python dimension-reduction
updated 6 months ago by 41k • written 4.0 years ago by ▴ 200
1
vote
1
reply
1.6k
views
Can cell ranger count take a folder of only .fastq.gz as input?
cellranger scRNAseq
updated 4.0 years ago by 13k • written 4.0 years ago by ▴ 200
3
votes
3
replies
2.3k
views
How much memory / how many cores should I request for peak calling?
ChIP-Seq slurm
updated 4.0 years ago by 136k • written 4.0 years ago by ▴ 200
3
votes
7
replies
2.1k
views
How should I use skewer to trim paired end reads?
ChIP-Seq skewer
4.0 years ago by jrleary ▴ 200
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