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Filtering for tag: scRNAseq • reset
0
votes
0
replies
30
views
Demultiplexing Samples With Contaminated Hashtag
scRNAseq seurat demultiplexing
1 day ago by fouerghi20 ▴ 30
0
votes
2
replies
88
views
integrate two single cell datasets and use transfer learning approach using annotated cell atlas
scRNASeq machine_learning
4 days ago by das2000sidd ▴ 30
0
votes
2
replies
113
views
heterogeneity in cluster when using Seurat Doheatmap
scRNAseq cluster r Seurat seurat
5 days ago by Jie • 0
0
votes
0
replies
64
views
Pathway enrichment analysis vs GSEA for single cell RNA sequencing data analysis
GSEA pathway scRNAseq
9 days ago by aa123 • 0
0
votes
1
reply
165
views
Seurat: Any way to identify genes expressed only in one condition of one cluster?
scRNAseq Seurat
updated 10 days ago by 9.2k • written 10 days ago by • 0
0
votes
1
reply
75
views
Help me solve this error in bigSCale2
bigSCale2 scRNAseq
updated 28 days ago by 5.4k • written 28 days ago by • 0
4
votes
9
replies
661
views
6 follow
Getting mitochondrial genes for scRNAseq
RNA-Seq rna-seq scRNAseq single-cell
updated 5 weeks ago by • 0 • written 9 months ago by • 0
0
votes
0
replies
95
views
DEG analysis between control and treatment groups in integrated scRNAseq analysis
scRNAseq integration DEG
5 weeks ago by aa123 • 0
1
vote
1
reply
142
views
zero inflated correlation computation scRNAseq
scRNAseq correlation
9 weeks ago by sim.j.baum ▴ 90
1
vote
2
replies
156
views
scRNAseq .h5ad (processed) data sets db?
single cell RNA seq data base scRNAseq snRNAseq
updated 10 weeks ago by 99k • written 10 weeks ago by ▴ 90
1
vote
2
replies
295
views
Duplicated row names on Seurat
CCLE Seurat scRNAseq single cell
updated 3 months ago by 20 • written 3 months ago by ▴ 30
0
votes
0
replies
172
views
Performing integration analysis of two datasets of different sizes in Seurat
scrnaseq seurat
3 months ago by aa123 • 0
1
vote
3
replies
229
views
Setting up scRNA-seq differential gene expression analaysis
scRNAseq differential gene expresion DEGs RNA-Seq
updated 4 months ago by 20 • written 5 months ago by • 0
0
votes
0
replies
2.0k
views
How to use "SingleR" on the marker genes from `FindAllMarkers` for each cluster?
SingleR seurat scRNAseq scRNA
4 months ago by SupBioInformatics ▴ 30
0
votes
3
replies
239
views
Normalization for subset of data
statistics scRNAseq
4 months ago by asumani ▴ 70
1
vote
6
replies
333
views
Single-cell RNA-seq coverage track not corresponding to gene structure
scRNAseq cellranger
updated 5 months ago by 5.1k • written 5 months ago by ▴ 100
0
votes
1
reply
276
views
Pooling WT and CRISPR/Cas9 KOs cells in the same scRNAseq sample and then demultiplex by puromycin resistance cassette expression
scRNAseq RNA-Seq CRISPR-CAS9
updated 5 months ago by ▴ 390 • written 5 months ago by ▴ 10
4
votes
2
replies
992
views
Finding Subclusters in Seurat Clusters
seurat scRNAseq cluster subcluster
updated 5 months ago by 9.2k • written 5 months ago by ▴ 30
1
vote
0
replies
322
views
Job: Two bioinformatics positions at Boston Children's Hospital
RNA-Seq next-gen bioinformatics scRNAseq Job
5 months ago by Liang Sun ▴ 10
0
votes
0
replies
245
views
mitochondria in single nuclear RNAseq
snrnaseq scrnaseq seurat single cell RNAseq
6 months ago by Rahul Tyagi • 0
1
vote
3
replies
511
views
iSEE singlecellexperiment GUI app on shinyapps not working, Troubleshooting
iSEE shiny scRNAseq
updated 6 months ago by ▴ 10 • written 6 months ago by ▴ 90
8
votes
11
replies
2.3k
views
How many PCs should be considered for downstream analyses?
scRNAseq PCA UMAP Clustering RNAseq
updated 6 months ago by ▴ 100 • written 13 months ago by ▴ 280
2
votes
3
replies
571
views
Running PHATE on Seurat Object
scRNAseq seurat PHATE
updated 6 months ago by 9.2k • written 6 months ago by ▴ 30
0
votes
8
replies
962
views
SCTransform prior or after merging samples into one object?
Seurat scRNAseq merging samples
6 months ago by annadv • 0
2
votes
11
replies
289
views
scRNAseq - DE
scRNAseq RNA-Seq DE
8 months ago by garciajessica0311 ▴ 10
0
votes
0
replies
217
views
TF regulatory network reconstruction from single cell
scRNAseq Seurat
updated 8 months ago by 11k • written 8 months ago by ▴ 250
0
votes
3
replies
459
views
scRNAseq: working with barcode, gene and matrix files
scRNAseq
updated 8 months ago by ▴ 570 • written 8 months ago by ▴ 110
4
votes
4
replies
1.4k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
9 months ago by Assa Yeroslaviz ★ 1.5k
0
votes
0
replies
306
views
Filtering out mouse cells based on mouse/human genes ratio
RNA-Seq scRNAseq 10x cellranger
9 months ago by biostarukha ▴ 10
2
votes
0
replies
424
views
Tool: CIPR - Cluster Identity Predictor for scRNAseq experiments
RNA-Seq R shiny scRNAseq Tool
10 months ago by atakanekiz ▴ 260
9
votes
11
replies
1.1k
views
Using limma for scRNAseq data
scRNAseq limma
updated 10 months ago by 12k • written 10 months ago by • 0
0
votes
1
reply
1.5k
views
Difference between "LogNormalize" normalization method in Seurat and z score normalization
z-score statistics normalization seurat scRNAseq
updated 11 months ago by 47k • written 11 months ago by • 0
2
votes
5
replies
243
views
gene expression correlation positive controls scRNAseq
scRNAseq gene expression correlation
updated 11 months ago by 11k • written 11 months ago by ▴ 830
0
votes
2
replies
824
views
Amazon AWS setup for the bioinformatic analysis particularly scRNAseq
AWS Rstudio scRNAseq
updated 11 months ago by 72k • written 11 months ago by ▴ 50
0
votes
0
replies
287
views
Adding certain barcodes to metadata
seurat scrnaseq
11 months ago by michelle.piquet ▴ 50
19
votes
18
replies
1.7k
views
about batch correction in scRNA-seq
scRNAseq scRNA batch correction
12 months ago by Bogdan ★ 1.1k
0
votes
3
replies
317
views
ConsensusClusterPlus error "Memory limit reached"
scRNAseq ConsensusClusterPlus
12 months ago by joker33 ▴ 30
6
votes
8
replies
428
views
using distinct versions of SEURAT on a SLURM cluster
Seurat scRNAseq
updated 12 months ago by 27k • written 14 months ago by ★ 1.1k
1
vote
4
replies
504
views
How to understand the multi-sample processing of Seurat?
RNA-Seq scRNAseq seurat
updated 12 months ago by 6.9k • written 13 months ago by ▴ 50
2
votes
0
replies
843
views
Job: Postdoctoral Scientist Position in Computational Biology at University of Missouri
scRNAseq job postdoc ChIP-Seq Job
12 months ago by Obi Griffith 19k
3
votes
5
replies
542
views
Downloading FASTQ files from ArrayExpress very slow
sequencing scRNAseq ArrayExpress FASTQ
12 months ago by f.morgana • 0
0
votes
2
replies
800
views
Normalization of index sort data in Seurat
R scRNAseq
13 months ago by f.morgana • 0
5
votes
5
replies
1.1k
views
Downsampling one of the sample on the UMAP clustering to match the number of cells of the other group
scRNAseq UMAP downsampling RNAseq
updated 13 months ago by 9.2k • written 13 months ago by ▴ 280
12
votes
14
replies
652
views
Identifying tumor cells in single cell RNAseq data
cancer scRNAseq R
updated 13 months ago by 9.2k • written 14 months ago by ▴ 170
3
votes
2
replies
1.3k
views
Any recommendations for copy number variation (CNV) packages for scRNA-seq?
single cell scRNAseq CNV R
updated 14 months ago by 9.2k • written 14 months ago by ▴ 170
0
votes
1
reply
286
views
Should cells be rows or columns when dimension reducing scRNAseq data?
scRNAseq single cell analysis
15 months ago by jrleary ▴ 170
1
vote
2
replies
1.0k
views
single cell RNA seq gene co-expression
scRNAseq gene co-expression
15 months ago by guillaume.rbt ▴ 830
4
votes
4
replies
1.4k
views
How to scale data for scater plotHeatmap function similar to Seurat?
scRNAseq scater Seurat heatmap
updated 15 months ago by 20 • written 17 months ago by ▴ 40
0
votes
0
replies
986
views
How to calculate pseudo time for all cells with monocle3
scRNAseq monocle3
16 months ago by xiaoguang ▴ 50
1
vote
1
reply
794
views
Can cell ranger count take a folder of only .fastq.gz as input?
cellranger scRNAseq
updated 16 months ago by 9.7k • written 16 months ago by ▴ 170
79 results • Page 1 of 2
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Comment: Bioinformatics startup market analysis
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Comment: How to download raw sequence data from GEO/SRA by cicindel ▴ 60
I tried to use the SRA toolkit a few months ago, I succesfully installed it and used `prefetch` to get the data, as per their tutorial, but…
Comment: Concatenating fasta files based on prefix ? by cpad0112 15k
If each group has `._1_1.txt.fa` and the pattern is exactly same as in OP, try this: ls *1_1.txt.fa | while read line; do echo ${line%…
Comment: Bioinformatics startup market analysis by grant.hovhannisyan ★ 2.1k
good luck!
Comment: Bioinformatics startup market analysis by gtechbio ▴ 30
Dear @juanjo75es, thank you for your input. We do agree that NGS data/metadata should be more accessible to public, in part also due to ini…
Comment: Bioinformatics startup market analysis by gtechbio ▴ 30
Dear @grant.hovhannisyan, thank you for the advice. In fact we are already in touch with two local genomics facilities, though as you have …
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Try raising your p-value to make sure that they aren't all just being filtered out by that threshold (which seems pretty low). Edit: I may…
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It looks like the following: system(paste0("mafft --anysymbol --maxiterate 1000 Alignment_output/",GENE,".fa > ",GENE,".mafft.fa")) GE…
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Yes, I am using the following loop first in R to process all the files. This is the code that I am running first: blastn.filelist <- s…
Comment: Bioinformatics startup market analysis by grant.hovhannisyan ★ 2.1k
agreed, especially if no private information (names, clinical status, etc) is needed, this information should be freely accessible.
Comment: question when using topgo by Kevin Blighe 72k
^^ this
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The GenTable() function has a parameter called *numChar* that controls this: "the GO term definition will be truncated such that only the f…
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See the 'is_a' field in the go.obo file. If you're looking for all subcategories of GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl…
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What does your `system()` command look like now, after having added `--anysymbol`? I am guessing you added `--anysymbol` right before that …
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Are you using this statement in a loop? If so, please refine your command to error out with the file that produces the error - maybe print …
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