User: David_emir

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David_emir370
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Posts by David_emir

<prev • 165 results • page 1 of 17 • next >
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GSVA analysis between Clusters
... Hi All, I am currently working on Tumor Normal Single-cell dataset (10X droplets) using Seurat protocol. I am interested in finding the differences in pathway activities scored per cell by GSVA(Gene set variation analysis) between the different clusters of a cell type (epithelial subtype). one [PAP ...
gsva single cell seurat written 13 days ago by David_emir370 • updated 13 days ago by khorms110
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Exporting Raw counts into .csv file from seurat object
... Hi All, I need to save Raw counts into .csv file from my Seurat object, I have tried the following code but it is not working for me expr_raw <- GetAssayData(object = alldata, assay.type = "RNA", slot = "counts") expr <- as(Class = 'matrix', object = expr_raw) It gives the following ...
csv raw counts seurat written 7 weeks ago by David_emir370 • updated 5 weeks ago by ccruizm.mv10
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Comment: C: Subsetting - Raw Counts from Seurat Object
... Thanks a lot for the reply, i just checked its shows the following > counts <- alldata@assays$RNA@counts [,1] [1,] NA > dim(counts) [1] 22294 780 ...
written 9 weeks ago by David_emir370
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Subsetting - Raw Counts from Seurat Object
... Hi All, I am working on Single-cell dataset, I wanted to extract raw counts of clusters (Say cluster num 4,6,8) and save it as a csv file. but I am not able to do the same, I have used the following codes, alldata_epi <- subset(alldata, idents = c(1,23,5,18,22,15)) counts <- alldat ...
seurat rna-seq raw counts written 9 weeks ago by David_emir370
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Comment: C: Count Matrix from Single cell RNA
... Thanks, Genomax, I have gone through this, in this, they have not mentioned about merging samples. the example data is of 2,700 single cells that were sequenced on the Illumina NextSeq 500. What we have is 25 patients (Prostate cancer) data and 25 different matrix files of the same disease and each ...
written 3 months ago by David_emir370
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Count Matrix from Single cell RNA
... Hi All, We did Single Cell RNA data analysis from 25 diseased patients. The Vendor sent 25.MTX files to us. The files we received is as follows filtered_feature_bc_matrix ├── barcodes.tsv.gz ├── features.tsv.gz └── matrix.mtx.gz 0 directories, 3 files The data comes off t ...
count single cell rna analysis matrix written 3 months ago by David_emir370
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Comment: C: Can't open file 'features': [Errno 2] No such file or directory
... Thanks a lot, Collin, it is Perfectly working now! Thanks again for helping. Dave ...
written 4 months ago by David_emir370
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Comment: C: Can't open file 'features': [Errno 2] No such file or directory
... Hi Collin, Thanks a lot for the quick reply, I have added the path for 20/20+ as follows `export PATH=$PATH:/home/ateeqanees/Desktop/20_20/2020plus-1.2.2` and when i say "echo $PATH" : /home/ateeqanees/anaconda3/bin:/home/ateeqanees/miniconda3/envs/2020plus/bin:/home/ateeqanees/miniconda3/condabin: ...
written 4 months ago by David_emir370
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Comment: C: Cancer driver mutations Identification from VCFs
... Hi Collin, thanks a lot for your help, I need your help in 20/20+ algo,[here][1] Thanks a lot, Have a great day! Dave. [1]: https://www.biostars.org/p/423501/ ...
written 4 months ago by David_emir370
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Can't open file 'features': [Errno 2] No such file or directory
... Hi All, I am using 20/20 plus algorithms for the identification of driver mutations in my sample. while creating Simulated features I am facing an error. rule simFeatures: input: output_soma_freebayes/simulated_summary/chasm_sim_summary3.txt, output_soma_freebayes/simulated_summary/onc ...
20/20plus mafs random forest 2020plus written 4 months ago by David_emir370 • updated 4 months ago by Collin830

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Popular Question 12 months ago, created a question with more than 1,000 views. For Error RNA-seq data, TOPHAT
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