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Showing top results for tag: scRNAseq • reset
0
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1
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64
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Comparison of two similar datasets with SCENIC
scrnaseq scRNA-Seq SCENIC GRN compare
updated 22 hours ago by ▴ 860 • written 1 day ago by • 0
1
vote
5
replies
272
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How to automatically distinguish single vs. bulk GEO datasets (in ARCHS4 collection or in general) ?
scRNAseq
1 day ago by Alexander ▴ 20
4
votes
4
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189
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Can I perform scRNAseq data integration without loosing features?
scRNAseq anchor integration Seurat features
3 days ago by joker33 ▴ 60
0
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1
reply
88
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Quantify transcriptomic shift between two conditions for each cluster
scRNAseq seurat singlecell RNAseq
updated 3 days ago by ▴ 10 • written 8 days ago by • 0
0
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0
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54
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Does the normalization method affect scRNAseq data integration?
scran scuttle scRNAseq integration normalization data
4 days ago by joker33 ▴ 60
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0
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47
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Single cell data clustering by TRBV type
seurat scRNAseq t-cells
updated 8 days ago by 104k • written 8 days ago by • 0
4
votes
2
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137
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What does that dip in the density plot mean from a single cell data analysis?
seurat scRNAseq
updated 12 days ago by 7.3k • written 12 days ago by ▴ 100
0
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2
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214
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Integrate CITESeq reads to Seurat object
scRNAseq CITEseqCount Seurat CITEseq
updated 18 days ago by ▴ 10 • written 19 days ago by • 0
1
vote
0
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78
views
scRNA-seq datasets for different cell lines
scRNAseq
19 days ago by Alexander ▴ 20
1
vote
2
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216
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Filtering nuclear RNA expression instead of MT expression in Scanpy
filtering nRNA scanpy scRNAseq mtRNA
updated 21 days ago by 52k • written 22 days ago by • 0
0
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2
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138
views
Normalization/Scaling with sctransform in RStudio of scRNASeq data
vst normalization sctransform scRNASeq scaling
21 days ago by ConfusedSheep • 0
0
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1
reply
187
views
Job: Bioinformatics Scientist in the department of Research Technology at Tufts University
scRNASeq Python R genomics
updated 23 days ago by ▴ 220 • written 23 days ago by • 0
0
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0
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109
views
GSEA using DEG csv file obtained from seurat scRNA-seq data
GSEA scRNAseq dataframe seurat
updated 23 days ago by 104k • written 23 days ago by • 0
0
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0
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134
views
Job: Bioinformatics Scientist openings in Central Florida
metagenomics metabolomics scRNAseq proteomics DNAseq
23 days ago by qysl • 0
0
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0
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73
views
MAST with UMI data
scRNAseq Seurat MAST
24 days ago by Wocher33 • 0
3
votes
3
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188
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scRNAseq analysis with logNormCounts (scran/scuttle package) - log transformation with different log base?
scran log logNormCounts scuttle scRNAseq
updated 24 days ago by 52k • written 25 days ago by ▴ 60
2
votes
2
replies
144
views
Detecting RNA Editing in Single-Cell RNA-seq
scRNAseq RNAediting
29 days ago by fouerghi20 ▴ 30
2
votes
2
replies
147
views
Gene Regulatory Networks on Single Cell RNAseq Datasets
GRN Transcription scRNAseq ChIPseq Factors
29 days ago by fouerghi20 ▴ 30
0
votes
1
reply
235
views
Job: Bioinformatician, Stem Cell Translational Lab, Div. of Preclinical Innovation, NCATS/NIH, Rockville, MD
transcriptomics scRNASeq genomics
updated 4 weeks ago by 34k • written 8 weeks ago by • 0
0
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2
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496
views
What is current the best available rat lung single cell RNA seq dataset for cell type annotation? any recommendations ?
SingleR scRNAseq
8 weeks ago by FantasticAI ▴ 30
0
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0
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65
views
Batch Effects in Multiplexed Perturbations
demultiplexing cellhashing singlecell scRNAseq
9 weeks ago by fouerghi20 ▴ 30
0
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0
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172
views
I use SingleR to get cell type annotation for each cell, then try to annotate each cluster, but the clustering result seems not to be consistent with…
SingleR scRNAseq
9 weeks ago by FantasticAI ▴ 30
2
votes
6
replies
498
views
What does it mean of de.genes in SingleR output? What is the difference between the genes in de.genes and genes in findMarkers?
SingleR scRNAseq
8 weeks ago by FantasticAI ▴ 30
3
votes
5
replies
410
views
Single cell analysis
TCGA R singlecellanalysis scRNAseq
10 weeks ago by leticia ▴ 20
4
votes
3
replies
411
views
How to plot the heat map of a subset of cell types using plotHeatmap from scater package
scRNAseq scRNA SingleR plotHeatmap scater
10 weeks ago by FantasticAI ▴ 30
0
votes
0
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74
views
Is there an existing function which averages gene expression across cells which I wish to pool?
scRNA-seq singlecellRNAseq RNA-Seq scRNAseq
10 weeks ago by Sanjay • 0
0
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0
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113
views
ANOVA for eliminating genes with low variance for scRNASeq data
scrnaseq pca variance anova
updated 10 weeks ago by 52k • written 10 weeks ago by • 0
0
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3
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207
views
i need help mouse prostata single cell data
scRNAseq porstate mouse
updated 10 weeks ago by 33k • written 10 weeks ago by • 0
0
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2
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235
views
Bam File Barcodes and UMIs not Formatted Correctly For Variant Calling
bam scRNAseq .bam vcf variant
updated 9 weeks ago by • 0 • written 10 weeks ago by • 0
2
votes
3
replies
345
views
is it normal to have zero mitochondria genes counts in my 10X data which is from Cellranger 5.0 count?
10X scRNAseq
updated 11 weeks ago by 5.4k • written 11 weeks ago by ▴ 30
1
vote
5
replies
278
views
How to ID cell types using reference scRNAseq dataset
Seurat groups scRNAseq
11 weeks ago by FantasticAI ▴ 30
1
vote
2
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275
views
Does cellranger count require index fastqs
scRNAseq 10x cellranger
updated 12 weeks ago by 104k • written 12 weeks ago by ▴ 20
0
votes
1
reply
231
views
MAST differential expression with batch information
scrnaseq single-cell MAST seurat batch-effect
updated 3 months ago by 52k • written 3 months ago by • 0
0
votes
1
reply
199
views
Technical single-cell question
RNAseq singlecell seurat scRNAseq
updated 3 months ago by 52k • written 3 months ago by • 0
0
votes
2
replies
242
views
scRNASeq equal number of cells across conditions
scRNAseq seurat
updated 3 months ago by 52k • written 3 months ago by ★ 4.4k
0
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2
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228
views
integrate two single cell datasets and use transfer learning approach using annotated cell atlas
scRNASeq machine_learning
3 months ago by das2000sidd ▴ 30
0
votes
2
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395
views
heterogeneity in cluster when using Seurat Doheatmap
scRNAseq cluster r Seurat seurat
3 months ago by Jie • 0
0
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0
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154
views
Pathway enrichment analysis vs GSEA for single cell RNA sequencing data analysis
GSEA pathway scRNAseq
3 months ago by aa123 • 0
0
votes
1
reply
437
views
Seurat: Any way to identify genes expressed only in one condition of one cluster?
scRNAseq Seurat
updated 3 months ago by ★ 11k • written 3 months ago by • 0
0
votes
1
reply
132
views
Help me solve this error in bigSCale2
bigSCale2 scRNAseq
updated 4 months ago by 5.5k • written 4 months ago by • 0
4
votes
9
replies
1.1k
views
6 follow
Getting mitochondrial genes for scRNAseq
RNA-Seq rna-seq scRNAseq single-cell
updated 4 months ago by • 0 • written 12 months ago by • 0
0
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0
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203
views
DEG analysis between control and treatment groups in integrated scRNAseq analysis
scRNAseq integration DEG
4 months ago by aa123 • 0
1
vote
1
reply
183
views
zero inflated correlation computation scRNAseq
scRNAseq correlation
5 months ago by sim.j.baum ▴ 110
1
vote
2
replies
278
views
scRNAseq .h5ad (processed) data sets db?
single cell RNA seq data base scRNAseq snRNAseq
5 weeks ago by sim.j.baum ▴ 110
1
vote
2
replies
557
views
Duplicated row names on Seurat
CCLE Seurat scRNAseq single cell
updated 6 months ago by 20 • written 7 months ago by ▴ 30
0
votes
0
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319
views
Performing integration analysis of two datasets of different sizes in Seurat
scrnaseq seurat
6 months ago by aa123 • 0
1
vote
3
replies
315
views
Setting up scRNA-seq differential gene expression analaysis
scRNAseq differential gene expresion DEGs RNA-Seq
updated 7 months ago by 20 • written 8 months ago by • 0
0
votes
0
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2.3k
views
How to use "SingleR" on the marker genes from `FindAllMarkers` for each cluster?
SingleR seurat scRNAseq scRNA
8 months ago by SupBioInformatics ▴ 50
0
votes
3
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357
views
Normalization for subset of data
statistics scRNAseq
8 months ago by asumani ▴ 70
1
vote
6
replies
499
views
Single-cell RNA-seq coverage track not corresponding to gene structure
scRNAseq cellranger
updated 8 months ago by 5.4k • written 8 months ago by ▴ 120
50 results • Page 1 of 1
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Answer: What's the biggest thing you dislike about bioinformatics?
Comment: opening downloaded files from STRING protein network without R
Comment: What's the biggest thing you dislike about bioinformatics?
Gene Set Enrichment Analysis
Comment: Removing genes of Seurat object during integration pipeline
How to generate a .sam/.bam file of a particular chromosome or even a particular region?
How To Split A Bam File By Chromosome
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Recent Replies
Comment: inquiry related to snpsift by rheab1230 • 0
the command: java -jar SnpSift.jar annotate dbSnp144.vcf variants.vcf > variants_annotated.vcf I am getting no error. the input file …
Comment: Displaying points which fall outside of the plot window in EnhancedVolcano by os306 ▴ 10
Hi there, just to follow up on this, I used your package to generate my volcano plots and got exactly what I was looking for. I now wish to…
Comment: inquiry related to snpsift by Kevin Blighe 75k
Hi, please show: 1. the command(s) that you are using 2. a sample of your input data 3. a sample of your output data 4. any status, wa…
Comment: opening downloaded files from STRING protein network without R by fionajcunningham • 0
thanks GenoMax I will try this sorry for delay in reply!! Fiona
Comment: What's the biggest thing you dislike about bioinformatics? by WouterDeCoster 45k
The alternative, constant off-by-one errors, aren't my idea of fun either :-)
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
Yeah, you can filter min_cells in Seurat with SCtransform. That would probably change the gene numbers in the SCT assay of the object. I u…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
Doesn't sctransform has a `min_cells` parameter that you could use here? It will only consider genes detected in at least `min_cells` cells…
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
I was thinking of making it an arbitrary cut off of 10 cells, Seurat's documentation uses 3 for reading in a single sample. I believe that …
Answer: How To Split A Bam File By Chromosome by etiennedanis • 0
With samtools v1.11, ```samtools view -b in.bam chr1 > out.bam``` did not work for me. But ```samtools view -b in.bam 1 > out.bam``` wo…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
What is a "few" cells? So how many? You would need to manually calculate the fraction of cells expressing a certain gene. Not sure in which…
Comment: I want to make a graph for conserved regions by sa.youssef • 0
Thanks so much, it is a great suggestion. may I ask you if you know a way to visualize the results of these data in my report? as we are wo…
Comment: Minfi - estimateCellCounts by Papyrus ★ 1.1k
I understand that you have whole blood samples and that's why you expect them to have more granulocytes? You could also try the [ENmix][1] …
Comment: error related to SnpSift by rheab1230 • 0
I am able to do this. I downloaded the .tar file instead of using conda
Comment: What's the biggest thing you dislike about bioinformatics? by Ram 34k
I'll join you. I am not a fan of python either.
Comment: SNP filtering by Ram 34k
Please pay close attention to [the command I wrote initially][1]. The correct command is `tabix -p vcf GEUVADIS.chr1.genotype.vcf.gz` The `…
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