User: kanwarjag

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kanwarjag890
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890
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Trusted
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United States
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1 week, 4 days ago
Joined:
5 years, 5 months ago
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k********@gmail.com

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Posts by kanwarjag

<prev • 307 results • page 1 of 31 • next >
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Similar samples in RNAseq
... I have a data set of 5 RNAseq samples and want to see which samples are close to stem cell population corresponding to one sample. What should be the best option to perform such analysis? If I have to perform unsupervised clustering then will SD will be good parameter to select most variable genes ...
rna-seq written 12 days ago by kanwarjag890
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identification of cell lineage tools
... Is there a tool that can help me to identify cell lineage from differential expression of genes? Thanks ...
rna-seq written 4 months ago by kanwarjag890 • updated 4 months ago by igor6.0k
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Comment: A: pathway for single cell RNA-seq
... I have already analyzed the data and has top differentially expressed genes specific for each cluster. Instead of using known markers I want to use enrichment/ pathway analysis that what type of cells are in each cluster. Apology If my original question was not explained clearly. ...
written 4 months ago by kanwarjag890
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pathway for single cell RNA-seq
... I have a single cell RNA-seq data form 10X genomics. I want to perform pathway analysis of top 50 genes of each cluster on the the basis of DE. These clusters represent cells with similar expression of genes. So in pathway analysis of these top 50 genes I want to identify what possible type of cell ...
pathway written 4 months ago by kanwarjag890 • updated 4 months ago by igor6.0k
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Comment: C: Question about Colon and small intestine size
... This appears to be a high school assignment. Try to google all this. ...
written 5 months ago by kanwarjag890
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Question about generalized linear model fitting
... I am analyzing a scRNAseq data trying to follow a protocol suggested in this paper- https://www.nature.com/articles/nature24489 mentioned under Computational analysis The statement reads- " Selection of variable genes was performed by fitting a generalized linear model to the relationship between t ...
rna-seq written 5 months ago by kanwarjag890 • updated 5 months ago by Kevin Blighe19k
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ScRNAseq and mitochondrial genes
... In single cell RNA seq mitochondrial (percentage of total expressed genes) is taken as a control. It is considered that less percentage of mitochondrial genes is indicative of good quality data. I could not find any rational when I google it or reading recent ScRNA-seq papers. Any pointer will be v ...
rna-seq written 5 months ago by kanwarjag890
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Comment: C: iontorrent RNAseq alignment
... TMAP is quite frequently used (https://github.com/iontorrent/TMAP) However I have used successfully TopHat (now HISAT). ...
written 5 months ago by kanwarjag890
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Question about a plot of RNAseq
... I was wondering is there any tool or method that can generate Fig 5A of https://www.nature.com/articles/ncomms14049?WT.feed_name=subjects_genetics. I know it is generated in moncole/ cell ranger/ surat, however if I have matrix than i may be able to draw it with any other tool and may have control ...
rna-seq written 5 months ago by kanwarjag890
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Question about mapping motif binding sites to genome location
... I have a naïve but complex question. I used RSAT to get 5 genes -2000 bp upstream sequence of TSS. I used this FASTA file and binding motif (identified from my experiment) in FIMO to see where is the binding site of the identified motif. I know that protein of interest bound very close to TSS. I g ...
genome written 7 months ago by kanwarjag890 • updated 6 months ago by Biostar ♦♦ 20

Latest awards to kanwarjag

Popular Question 3 months ago, created a question with more than 1,000 views. For DEseq/ EdgeR RNaseq calculation of fold change
Popular Question 3 months ago, created a question with more than 1,000 views. For RPKM to FPKM conversion
Popular Question 3 months ago, created a question with more than 1,000 views. For log ratio in gene expression array
Popular Question 3 months ago, created a question with more than 1,000 views. For lift-over hg19 to GRch38
Popular Question 3 months ago, created a question with more than 1,000 views. For Is Genotype Info Must While Validating Mutations
Popular Question 3 months ago, created a question with more than 1,000 views. For co-expression of genes in normal and cancer
Great Question 3 months ago, created a question with more than 5,000 views. For Converting Protein Names To Gene Ids
Popular Question 3 months ago, created a question with more than 1,000 views. For pllotting tag density across TSS and TES
Popular Question 3 months ago, created a question with more than 1,000 views. For heatmap for a predetermined order of rows
Popular Question 3 months ago, created a question with more than 1,000 views. For CPG island annotation with gene
Popular Question 3 months ago, created a question with more than 1,000 views. For Is Genotype Info Must While Validating Mutations
Popular Question 3 months ago, created a question with more than 1,000 views. For Is Genotype Info Must While Validating Mutations
Popular Question 4 months ago, created a question with more than 1,000 views. For breast cancer subtype
Popular Question 4 months ago, created a question with more than 1,000 views. For Is Genotype Info Must While Validating Mutations
Popular Question 5 months ago, created a question with more than 1,000 views. For Is Genotype Info Must While Validating Mutations
Appreciated 5 months ago, created a post with more than 5 votes. For iontorrent RNAseq alignment
Popular Question 5 months ago, created a question with more than 1,000 views. For breast cancer subtype
Popular Question 5 months ago, created a question with more than 1,000 views. For Is Genotype Info Must While Validating Mutations
Popular Question 5 months ago, created a question with more than 1,000 views. For Is Genotype Info Must While Validating Mutations
Popular Question 7 months ago, created a question with more than 1,000 views. For pllotting tag density across TSS and TES
Popular Question 7 months ago, created a question with more than 1,000 views. For lift-over hg19 to GRch38
Popular Question 7 months ago, created a question with more than 1,000 views. For heatmap for a predetermined order of rows
Popular Question 7 months ago, created a question with more than 1,000 views. For RPKM to FPKM conversion
Popular Question 7 months ago, created a question with more than 1,000 views. For breast cancer subtype
Popular Question 7 months ago, created a question with more than 1,000 views. For Is Genotype Info Must While Validating Mutations

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