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Showing top results for tag: scrna-seq • reset
1
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2
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120
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When to use integration with scRNASeq
R SEURAT scRNA-seq
16 hours ago by Varun Gupta ★ 1.3k
0
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0
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174
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Can I use a dataset that has batch effect as a reference in scmap?
scRNA-seq annotation
8 days ago by D • 0
0
votes
1
reply
249
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Harmony integration of integarted samples
scRNA-seq harmony
updated 10 days ago by ★ 17k • written 10 days ago by ▴ 70
1
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0
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145
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Calculating if cell proportions are significant using propeller
regression proportions scRNA-seq
12 days ago by mropri ▴ 160
0
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7
replies
511
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Chromium 5’ Next GEM single cell STARsolo
10x STAR scRNA-seq
updated 16 days ago by ★ 6.8k • written 18 days ago by • 0
4
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13
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761
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Can't reproduce harmony results in Seurat
Seurat scRNA-seq harmony
14 days ago by fifty_fifty ▴ 70
0
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3
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468
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Weird outcomes from employing NMF on scRNA-seq data
NMF scRNA-seq
updated 19 days ago by ▴ 430 • written 24 days ago by ▴ 130
1
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0
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298
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How to identify temporal differential gene expression patterns among cell types in scRNA-seq
gene-expression dynamic scRNA-seq DEGs
updated 21 days ago by 44k • written 22 days ago by ★ 1.3k
1
vote
3
replies
544
views
Integrate several multiome objects
scATAC-seq multiome Seurat scRNA-seq
updated 26 days ago by 145k • written 4 weeks ago by ▴ 10
1
vote
2
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281
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Extracting normalized counts from RDS (Seurat) file
seurat scRNA-seq harmony snRNA-seq
updated 26 days ago by ★ 4.3k • written 26 days ago by • 0
1
vote
2
replies
409
views
GSEA single cell
gsea scRNA-seq
updated 26 days ago by ★ 4.3k • written 4 weeks ago by ▴ 10
0
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2
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283
views
CCA integration
single-cell scRNA-seq batch-correction
26 days ago by kayah ▴ 20
4
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6
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530
views
Batch correction preserving biological difference
scRNA-Seq batch-correction
4 weeks ago by foejvs546 ▴ 20
1
vote
1
reply
240
views
Gene Regulatory Network Inference Data Needed
GRN scATAC-SEQ scRNA-SEQ Single-Cell Gene-Regulatory-Networks
updated 5 weeks ago by 44k • written 5 weeks ago by ▴ 110
1
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4
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698
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 5 weeks ago by ▴ 90 • written 5 months ago by ▴ 20
3
votes
6
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581
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normalization in single cell
normalization scRNA-seq single-cell
updated 5 weeks ago by 5.6k • written 6 weeks ago by ▴ 20
0
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0
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120
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Using Arriba on single cell data set (scRNA-seq)
scrna-seq
5 weeks ago by sogand • 0
0
votes
2
replies
238
views
low ribosomal protein in scrnaseq data
ribosomal-proteins scRNA-seq
updated 5 weeks ago by 44k • written 5 weeks ago by • 0
3
votes
2
replies
400
views
Integration of scRNA-seq datasets from different tissues
scRNA-seq
updated 6 weeks ago by ▴ 90 • written 9 weeks ago by • 0
0
votes
1
reply
330
views
miloR - object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance
seurat scRNA-seq miloR
updated 7 weeks ago by 145k • written 4 months ago by ▴ 10
0
votes
1
reply
330
views
Unable to open HDF5 file
HDF5 Seurat scRNA-Seq
updated 7 weeks ago by ★ 3.0k • written 7 weeks ago by • 0
0
votes
1
reply
297
views
When should I normalize and subset adata objects in scanpy?
scanpy scRNA-seq single-cell
updated 7 weeks ago by 4.3k • written 7 weeks ago by ▴ 150
0
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0
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147
views
Automatically annotate gene loci
reference-genome scRNA-seq gene-annotation
updated 8 weeks ago by 44k • written 8 weeks ago by ▴ 80
2
votes
2
replies
1.4k
views
Subsetting cells from a previously integrated Seurat dataset (scRNA-seq)
Subclustering scRNA-seq Seurat
updated 8 weeks ago by • 0 • written 18 months ago by ▴ 10
0
votes
2
replies
380
views
Pseudobulk for scRNA-seq: sum or mean?
scRNA-seq pseudobulk
updated 9 weeks ago by ★ 4.3k • written 9 weeks ago by • 0
0
votes
1
reply
254
views
How to choose cells that co-express several genes with scanpy?
scanpy scRNA-seq single-cell
updated 9 weeks ago by 4.3k • written 9 weeks ago by ▴ 150
2
votes
5
replies
650
views
10X #3' RNA seq - How is strandedness determined?
scRNA-seq
updated 11 weeks ago by 44k • written 11 weeks ago by • 0
1
vote
2
replies
690
views
Forum: scRNA-seq: Do people eliminate housekeeping genes for the sake of increasing algorithmic efficiency (and this speed)?
housekeeping-genes scRNA-seq
updated 11 weeks ago by 44k • written 12 weeks ago by • 0
11
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9
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2.8k
views
8 follow
Why it is not use UMIs for RNA-seq?
RNA-Seq UMIs scRNA-seq
updated 12 weeks ago by ▴ 30 • written 3.9 years ago by ★ 1.3k
1
vote
1
reply
286
views
Differential expression bias in Seurat
markers seurat scRNA-seq single-cell
updated 3 months ago by ★ 17k • written 3 months ago by • 0
2
votes
0
replies
341
views
Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
RNA-seq scRNA-seq
updated 3 months ago by 44k • written 3 months ago by ▴ 20
15
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4
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788
views
How to identify cell identities in mixed scRNA-seq using mutational signatures from bulk RNA-seq
RNA-seq scRNA-seq
3 months ago by Chilly ★ 1.3k
0
votes
0
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264
views
News: ONLINE COURSE – Introduction to Single Cell Analysis (ISCA01)
Trailmaker Single-cell RNA-seq scRNA-seq
updated 3 months ago by 44k • written 3 months ago by ▴ 110
0
votes
0
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171
views
Define outliers in proportional difference in scRNAseq analysis
scRNA-seq
updated 3 months ago by 44k • written 3 months ago by • 0
1
vote
1
reply
251
views
glmGamPoi offset matrix details
glmGamPoi RNA-seq scRNA-seq
updated 3 months ago by 84k • written 3 months ago by • 0
0
votes
2
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531
views
Should I normalize and scale my data again after doing subset(seu, idents=" ") in Seurat?
normalization seurat scRNA-seq
3 months ago by ev97 ▴ 30
1
vote
2
replies
371
views
Shallow sequencing is not a random subsample of deep sequencing
Illumina scRNA-seq
3 months ago by jockbanan ▴ 440
0
votes
1
reply
367
views
cellranger error fix GTF
gtf cellranger scRNA-seq
updated 3 months ago by 44k • written 3 months ago by ▴ 150
5
votes
4
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479
views
Statistical test to compare cell type proportions in scrnaseq data
compositional-analysis scRNA-seq
3 months ago by sarahmanderni ▴ 120
0
votes
7
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767
views
Download SRR by parallel and fastq dump with a weird problem
scRNA-seq linux parallel
3 months ago by diqixiaoyaoer ▴ 20
2
votes
0
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329
views
Tutorial: Seurat Object Explained: Beginner's Guide and Demo
scRNA-seq Seurat single-cell
updated 3 months ago by 44k • written 3 months ago by ★ 4.3k
1
vote
3
replies
422
views
How to do preprocessing from fastqc
fastqc scRNA-seq single-cell
updated 3 months ago by 44k • written 3 months ago by • 0
2
votes
3
replies
788
views
Is it possible to modify the gene names from the x-axis in Seurat::Dotplot?
seurat scRNA-seq single-cell dotplot
updated 3 months ago by 44k • written 3 months ago by ▴ 30
2
votes
2
replies
407
views
Finding DEGs of cell type comprising of more than one clusters
DEG FindAllMarkers scRNA-seq single-cell
updated 3 months ago by 44k • written 3 months ago by • 0
0
votes
2
replies
654
views
Speed of Cell-Cell interaction analysis on scRNA-seq data
Cellchat scRNA-seq Seurat
updated 3 months ago by ▴ 190 • written 15 months ago by ▴ 10
0
votes
1
reply
358
views
Editing seurat object metatdata
Seurat metadata scRNA-seq
updated 3 months ago by ▴ 90 • written 3 months ago by • 0
1
vote
0
replies
259
views
Tutorial: SingleCellExperiment object explained with a real-world example
bioconductor scRNA-seq single-cell
updated 3 months ago by 44k • written 3 months ago by ★ 4.3k
0
votes
4
replies
486
views
Test custom signature using GSEA in scRNA-seq
scRNA-seq Seurat GSEA
3 months ago by bio_info ▴ 20
0
votes
1
reply
285
views
Query regarding single cell rna seq annotation using marker genes
scRNA-seq
updated 3 months ago by 44k • written 3 months ago by • 0
0
votes
2
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316
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SCPA analysis with all qvals = 0
scRNA-seq SCPA Seurat
3 months ago by bio_info ▴ 20
50 results • Page 1 of 1
Recent Votes
Comment: When to use integration with scRNASeq
Answer: Using GEOquery
Answer: Using GEOquery
Comment: Using GEOquery
Comment: Using GEOquery
Comment: Using GEOquery
Comment: how to get visium HD dataset with its information
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Comment: how to get visium HD dataset with its information by Nat.Nataren ▴ 90
Might also be worth looking at the CELLxGENE database and selecting Visium datasets. The corresponding publication may provide the addition…
Comment: Mendelian precison by heureuse • 0
Not for that but to know the % of CNV inherited in order to know the sensitivity of the caller
Comment: Mendelian precison by heureuse • 0
This is really helpful and beyond what I've expected. Thank you
Answer: featureCounts segmentation fault by Jaber • 0
Thank you, I already extracted manually, as I am using WSL, and directories are correct, and I still get the error saying "Segmentation fa…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
Thx. I found out that I used the wrong reference genome. I have a set of data from mice and a set from humans. I processed the human data u…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
Thx. It turns out that the file was damaged during transmission.
Comment: how to get visium HD dataset with its information by GenoMax 145k
Depending on how much of that information is personally identifiable you may not be able to get the metadata unless you get approval from d…
Comment: HTseq count issue, not aligning to features by GenoMax 145k
Have you examined the alignments with IGV or a similar genome browser? Are the reads aligning in correct place (e.g. under exons). Also try…
Answer: featureCounts segmentation fault by Mensur Dlakic ★ 28k
It is very difficult to follow al the lines as your script content are not properly formatted. It appears that in one command you are do…
Comment: Using GEOquery by ATpoint 84k
Have you even read my answer? I gave a full explanation on what the problem is and what the solutions can be. What is unclear?
Comment: Using GEOquery by Rohulla • 0
I also come up with this problem. No body still answer this question.
Answer: Performing Needleman-Wunsch Global Alignment for multiple mutant proteins agains by Istvan Albert 101k
You can use the `bio` with the `align` tool. Install with `pip install bio` then bio align query.fa target.fa You can put all the tar…
Answer: Long-read sequencing data simulation using CAMISIM by Istvan Albert 101k
Since they explicitly have a pbsim config file, the comment you found is probably just a leftover from another config file that was copied …
Comment: RNA-Seq mutation calling without germline data by marionette.kent • 0
Thanks @shred for sharing your pipeline. Can I ask if it runs each sample individually? Our HPC has limited space for each user so I have b…
Comment: Pedigree information by bk11 ★ 3.0k
Since you have plink (bed/bim/fam) files, sex information is stored in the 5th column of the `.fam` file. If that information is missing an…
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