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Showing top results for tag: single-cell • reset
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News: ONLINE COURSE – Introduction to Single Cell Analysis (ISCA01)
Single-Cell scRNA-Seq
updated 15 days ago by 44k • written 15 days ago by ▴ 110
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7
replies
565
views
Unexplainable missing values in single cell Seurat object
seurat single-cell
updated 16 days ago by 44k • written 17 days ago by ▴ 10
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2
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337
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Single-cell RNA differential expression with an unbalanced number of cells between conditions
single-cell differential-expression
16 days ago by Javi.villegas21 • 0
0
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1
reply
213
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What are the epithelial cells subtype in esophagus tissue ?
python scanpy anndata single-cell
updated 23 days ago by 85k • written 23 days ago by ▴ 160
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7
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592
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ncRNA, pseudogenes and lncRNA genes in highly variable features ( scRNA)
single-cell
updated 4 weeks ago by ★ 6.9k • written 5 weeks ago by ▴ 40
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0
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166
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Keep seeing same degs everytime after filtering and clustering (scRNA)
single-cell
updated 5 weeks ago by 44k • written 5 weeks ago by ▴ 40
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3
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369
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Variant callers for single cell WGS
variant Single-cell WGS
5 weeks ago by Binny • 0
2
votes
1
reply
353
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Best approach for identifying top proteins in a single cluster in single-cell analysis
ADT CITEseq Single-cell Seurat
updated 5 weeks ago by ★ 3.0k • written 5 weeks ago by ▴ 10
0
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1
reply
293
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Noise confounding genes in single cell data
single-cell
updated 5 weeks ago by 44k • written 5 weeks ago by ▴ 40
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3
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529
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Help Analysing Perturb-Seq Data - How do I extract 10X cell barcodes and relevant guides from fastq files?
Single-Cell Perturb-Seq 10X
updated 6 weeks ago by ▴ 600 • written 7 weeks ago by • 0
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2
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714
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Mapping Mouse RNAseq Marker Genes to Reactome Pathways
RNA-seq single-cell pathways reactome
updated 6 weeks ago by • 0 • written 11 months ago by ▴ 40
13
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23
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16k
views
11 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 6 weeks ago by • 0 • written 5.4 years ago by ★ 18k
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0
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235
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CellTypist Confidence Scores vs SingleR Delta Scores
single-cell singleR celltypeannotation celltypist
6 weeks ago by Manuel Sokolov Ravasqueira ▴ 110
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4
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564
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What should I do if death cell counts and types biologically important in my single cell data?
scRNA cell-death single-cell
updated 6 weeks ago by 44k • written 6 weeks ago by ▴ 40
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2
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308
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CCA integration
single-cell scRNA-seq batch-correction
8 weeks ago by kayah ▴ 20
3
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1
reply
424
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Chemistry Detection Error in CellRanger for Single-Cell RNA-Seq Data
cellranger single-cell RNA
updated 8 weeks ago by 146k • written 8 weeks ago by ▴ 10
12
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6
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888
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Downloading paired end fastq data from SRA
SRA single-cell RNA-Seq
9 weeks ago by Matheus • 0
0
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3
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324
views
Single cell whole genome sequence
Single-cell WGS
updated 5 weeks ago by 146k • written 9 weeks ago by • 0
1
vote
0
replies
169
views
News: RNAseq and Single Cell Analysis Online Courses @ Edinburgh Genomics
RNA-seq single-cell workshop
updated 8 weeks ago by 44k • written 9 weeks ago by ▴ 10
1
vote
1
reply
260
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Gene Regulatory Network Inference Data Needed
GRN scATAC-SEQ scRNA-SEQ Single-Cell Gene-Regulatory-Networks
updated 9 weeks ago by 44k • written 9 weeks ago by ▴ 110
2
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3
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905
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Annotating single cell data automatically
single-cell
updated 10 weeks ago by ▴ 90 • written 6 months ago by ▴ 10
3
votes
6
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626
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normalization in single cell
normalization scRNA-seq single-cell
updated 10 weeks ago by 5.8k • written 10 weeks ago by ▴ 20
2
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2
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387
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Only two fastqs for 10X scATAC-seq data deposited on GEO database.
scATAC-seq cellranger single-cell 10X
10 weeks ago by 1048686151 • 0
0
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0
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198
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Using get_normalized_expression (scVI) vs. Log-Normalized Counts
scVI normalization RNA-seq single-cell UMAP
10 weeks ago by Nicolas • 0
2
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4
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1.6k
views
Create Seurat Object from matrix and two text files
Single-Cell RNA-Seq Seurat
updated 11 weeks ago by ▴ 10 • written 12 months ago by ▴ 10
0
votes
1
reply
334
views
When should I normalize and subset adata objects in scanpy?
scanpy scRNA-seq single-cell
updated 11 weeks ago by 4.3k • written 11 weeks ago by ▴ 150
1
vote
3
replies
3.2k
views
Remove column from Seurat metadata
single-cell transcriptomics cell-type-annotation RNAseq
updated 12 weeks ago by ▴ 40 • written 18 months ago by ▴ 30
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0
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277
views
Cell Typist Providing different results between iterations
Python Single-Cell CellAnnotation CellTypist
updated 3 months ago by 44k • written 3 months ago by ▴ 110
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0
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212
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SMART-seq normalizarion and integration
SMART-seq single-nuclei normalization RNA-seq single-cell
3 months ago by vigbr ▴ 20
0
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1
reply
278
views
How to choose cells that co-express several genes with scanpy?
scanpy scRNA-seq single-cell
updated 3 months ago by 4.3k • written 3 months ago by ▴ 150
2
votes
5
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402
views
Same sample and reference genome, different number of reads
STARsolo Single-cell RNAseq
updated 3 months ago by ★ 1.3k • written 3 months ago by • 0
0
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1
reply
313
views
How do I use msigdb to annotate the single cell data?
msigdb single-cell
updated 3 months ago by 44k • written 3 months ago by ▴ 100
1
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7
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662
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How do decide if a processed scRNA-seq data is read counts or UMI format ?
scanpy python single-cell anndata RNA
updated 3 months ago by 85k • written 3 months ago by ▴ 160
0
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0
replies
210
views
Cell-Cycle Variation in 10x Multiomics
seurat multiome 10x single-cell
updated 3 months ago by 44k • written 3 months ago by • 0
0
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0
replies
198
views
Can I use CEMiTool to analyze single cell RNA seq data?
CEMiTool single-cell
updated 3 months ago by 44k • written 3 months ago by • 0
0
votes
1
reply
363
views
Using Pseudobulk Approach for Identifying Marker Genes Within a Single Condition
differential-expression single-cell pseudobulk
updated 3 months ago by 85k • written 3 months ago by ▴ 430
0
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0
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211
views
T cell subtype annotation
seurat single-cell SingleCellExperiment
updated 3 months ago by 44k • written 3 months ago by • 0
1
vote
1
reply
306
views
Differential expression bias in Seurat
markers seurat scRNA-seq single-cell
updated 4 months ago by ★ 18k • written 4 months ago by • 0
0
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1
reply
287
views
Creating a Single-Cell Signature Matrix for Bulk RNA-seq Deconvolution
rna-seq signature deconvolution single-cell
updated 4 months ago by 44k • written 4 months ago by • 0
4
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3
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378
views
Any recommended way to view scRNAseq results in an interactive format?
RNA-seq single-cell
3 months ago by Pei ▴ 220
1
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2
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354
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How to install python package scMultiCluster_kmeans_totalVI?
conda gpu multiomics google-colab single-cell
4 months ago by KABILAN ▴ 100
0
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3
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502
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Where does cellranger log its estimates for the input to DETECT_COUNT_CHEMISTRY?
cellranger sequencing single-cell
updated 4 months ago by 85k • written 4 months ago by ▴ 300
4
votes
4
replies
620
views
How to install dependencies in conda environment in Google colab?
conda gpu multiomics google-colab single-cell
updated 4 months ago by 55k • written 4 months ago by ▴ 100
0
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0
replies
293
views
News: ONLINE COURSE – Introduction to Single Cell Analysis (ISCA01)
Trailmaker Single-cell RNA-seq scRNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 110
0
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1
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283
views
Does it make sense to do hdWGCNA following the DEG analysis?
DEG WGCNA single-cell
updated 3 months ago by • 0 • written 4 months ago by ▴ 90
0
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1
reply
402
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Downloading 10X Spatial Transcriptomic Data from GEO
GEO Spatial-Trascriptomics single-cell
updated 4 months ago by 146k • written 4 months ago by • 0
2
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4
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649
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Histogram of normalized counts for each cell type
seurat single-cell
4 months ago by odi ▴ 10
2
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6
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670
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Finding scRNA-seq datasets of healthy human ovaries
python GEO single-cell RNA
updated 4 months ago by 44k • written 4 months ago by ▴ 160
0
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0
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725
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News: Webinar: "Integrated analysis of single-cell data across technologies, modalities, and perturbations" by Rahul Satijia (author of Seurat)
integrated-analysis Seurat single-cell
updated 4 months ago by 44k • written 4 months ago by ▴ 60
0
votes
0
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185
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Cell fractions (from single cell) as variable in Cox Survival model
Cox single-cell
updated 4 months ago by 44k • written 4 months ago by ▴ 70
50 results • Page 1 of 1
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Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data by king • 0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation by Chen • 0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once? by GenoMax 146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset by allingt • 0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
Comment: dittoHeatmap; adding column labels on the heatmap by jared.andrews07 ★ 18k
I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type by allingt • 0
What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
Comment: Genes of Interest in a Multi-Tissue Analysis by allingt • 0
The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
Comment: WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendr by allingt • 0
Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
Comment: Why does WGCNA use weighted correlation instead of Pearson correlation? by allingt • 0
The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
Comment: dittoHeatmap; adding column labels on the heatmap by Varun Gupta ★ 1.3k
any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
Comment: How can I determine the p-value of genes within each identified module in WGCNA? by allingt • 0
What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is by i.sudbery 20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
Answer: Using NumReads column of quants.genes.sf file to build DESeq2 input by i.sudbery 20k
One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…
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