User: komal.rathi

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komal.rathi3.7k
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Location:
Children's Hospital of Philadelphia, Philadelphia, PA
Website:
https://github.com/kom...
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komalsrathi
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Last seen:
1 month, 2 weeks ago
Joined:
7 years, 9 months ago
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Posts by komal.rathi

<prev • 418 results • page 1 of 42 • next >
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Answer: A: using hclust object from FactoMineR::HCPC to force clustering in pheatmap
... Someone posted an answer to this on stackoverflow which I am sharing here: https://stackoverflow.com/a/63017471/1844024 To get the correct dendrogram, you need first to reorder the columns of tmp according to the information given in `pcahcpc.tree$labels`. idx <- as.numeric(gsub("col_","", ...
written 6 months ago by komal.rathi3.7k
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Comment: C: using hclust object from FactoMineR::HCPC to force clustering in pheatmap
... The pcahcpc.tree seems to be a valid hclust object: > class(pcahcpc.tree) [1] "hclust" ...
written 6 months ago by komal.rathi3.7k
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using hclust object from FactoMineR::HCPC to force clustering in pheatmap
... Cross posted: https://stackoverflow.com/questions/62972420/hclust-object-from-factorminer-does-not-cluster-dendrogram-in-pheatmap I am trying to create a heatmap of a matrix with 20 rows and 10 columns using `pheatmap::pheatmap`. To cluster the columns, I am using an `hclust` object obtained after ...
factorminer hcpc pca rna-seq written 6 months ago by komal.rathi3.7k
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Comment: C: snakemake: pipeline failed with MissingOutputException
... What versions of STAR/RSEM are you using? Also, can you do a `tree` (or show the directory structure) on your working directory? I see you have hardcoded the paths of `bam/, fastq/ and quant/`. Just want to make sure these directories exist. ...
written 14 months ago by komal.rathi3.7k
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Comment: C: Download all eQTL data for all the 9 tissues from GTEx Portal
... Can you move this to an answer so I can accept it? Thanks! ...
written 15 months ago by komal.rathi3.7k
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Answer: A: How to get known canonical transcript information from UCSC for a specific genco
... I got a response from the UCSC Genome Browser help desk which resolved my question: > The knownCanonical gene set is created from the longest transcript of > the basic Gencode gene set. This convention was not around for the V23 > gene set, so that file does not exist. If you would like to ...
written 20 months ago by komal.rathi3.7k
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Comment: C: How to get known canonical transcript information from UCSC for a specific genco
... Thanks, I will do that. I will keep this open and post any responses I get from the help desk. ...
written 20 months ago by komal.rathi3.7k
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How to get known canonical transcript information from UCSC for a specific gencode version
... Hi, I am using UCSC genome browser to get known canonical transcripts using this [link][1]. This is the default Gencode version V29 and I am able to set the `table` to `knownCanonical`. However, when I change the gencode version to `ALL Gencode V23` under `track`, the table options change and I can ...
gencode canonical transcripts ucsc written 20 months ago by komal.rathi3.7k
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Comment: C: GATK ASEReadCounter: Downstream analysis for identifying allele specific express
... I ended up doing a chisq test using the output of ASEReadCounter. ...
written 2.0 years ago by komal.rathi3.7k
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Comment: C: RSEM output interpretation
... I am using the following parameters: rsem-calculate-expression \ --paired-end \ --no-bam-output \ --quiet \ --no-qualities \ -p {threads} \ --forward-prob 0.5 \ --seed-length 25 \ --fragment-length-mean -1.0 \ --bam {bam} {genomedir} {prefix} ...
written 2.2 years ago by komal.rathi3.7k

Latest awards to komal.rathi

Scholar 5 months ago, created an answer that has been accepted. For A: cufflink and cuffmerge error
Prophet 5 months ago, created a post with more than 20 followers. For TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from controls?
Appreciated 5 months ago, created a post with more than 5 votes. For C: DEXSeq with cufflinks gtf file
Good Question 5 months ago, asked a question that was upvoted at least 5 times. For Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
Appreciated 6 months ago, created a post with more than 5 votes. For C: DEXSeq with cufflinks gtf file
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How the best way to verify the up and down regulated genes in a list of DE genes
Scholar 6 months ago, created an answer that has been accepted. For A: cufflink and cuffmerge error
Popular Question 6 months ago, created a question with more than 1,000 views. For DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Great Question 10 months ago, created a question with more than 5,000 views. For How to remove reads with hard/soft clipping along with its mate?
Popular Question 10 months ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Prophet 10 months ago, created a post with more than 20 followers. For TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from controls?
Popular Question 11 months ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: have difficults using htseq count
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: How the best way to verify the up and down regulated genes in a list of DE genes
Teacher 12 months ago, created an answer with at least 3 up-votes. For C: have difficults using htseq count
Popular Question 13 months ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Appreciated 15 months ago, created a post with more than 5 votes. For C: DEXSeq with cufflinks gtf file
Great Question 15 months ago, created a question with more than 5,000 views. For How To Get Mapping Statistics On Bam File
Scholar 15 months ago, created an answer that has been accepted. For A: Error in htseq-count: "Malformed SAM line: MRNM == '*' although flag bit &0x0008
Scholar 15 months ago, created an answer that has been accepted. For A: cufflink and cuffmerge error
Popular Question 17 months ago, created a question with more than 1,000 views. For DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Popular Question 17 months ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Popular Question 17 months ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Teacher 19 months ago, created an answer with at least 3 up-votes. For C: have difficults using htseq count
Scholar 19 months ago, created an answer that has been accepted. For A: cufflink and cuffmerge error

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