User: halo22

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halo22120
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Indianapolis, IN
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M.S. Bioinformatics 

Posts by halo22

<prev • 49 results • page 1 of 5 • next >
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How to use limma for a categorial outcome variable? Where outcome is the cohort status and predictor is gene expression.
... Hello All, I am very new to limma and trying to build a logistic regression like model using limma where my goal is to understand associations between the cohort status and gene expression while accounting for variables like age and sex. My gene expression is quantified using RSEM with TPM counts. ...
next-gen rna limma rna-seq written 11 weeks ago by halo22120 • updated 8 weeks ago by Biostar ♦♦ 20
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Comment: C: Reading methylation without IDAT files downloaded from GEO
... Thank you! I will reach out to the person who uploaded the data and ask for IDAT's. ...
written 8 months ago by halo22120
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Reading methylation without IDAT files downloaded from GEO
... Hello All, I am working on a GEO series methylation dataset (GSE*) that I have downloaded from the GEO site. The downloads include three different files, 1) GSE*_Matrix_methylated_signal_intensities.txt.gz 2) GSE*_Matrix_methylated_signal_intensities.txt.gz 3) GSE*_RAW.tar, since there is no IDAT ...
geo methylation minfi gene expression omnibus written 8 months ago by halo22120 • updated 8 months ago by Charles Warden6.8k
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Turning transcript estimate to gene level estimates
... Hello All, I've used the featureCounts program on my bam files to estimate the transcript counts(below is the code snippet). Since a single gene can have multiple transcripts associated with it. What would be the best way to calculate a gene level estimate? Can adding gene specific transcript c ...
next-gen rna-seq written 10 months ago by halo22120 • updated 10 months ago by Devon Ryan90k
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Analyzing data produced by the UMI based SCRB-seq (Soumillon et al. 2014) protocol.
... Hello All, I am working on analyzing single cell RNA-seq data generated using the SCRB-seq protocol. The data that I have has already gone through data pre-processing including demultiplexing the BCL files using Picard, alignment with STAR, QC with RNASeqQC and marking duplicates with UmiAwareMarkD ...
next-gen rna-seq written 10 months ago by halo22120 • updated 9 months ago by Biostar ♦♦ 20
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Generating a gene expression matrix from Picard *duplicates_marked.bam file
... Hello All, I am new to RNA sequencing analysis and trying to figure out what could be a better way to generate gene-expression matrix for my analysis with Picard output. I received the RNA dataset from a collaborator who has an internal pipeline that does the primary QC, alignment with STAR and seq ...
rna-seq written 10 months ago by halo22120
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10X based Single cell sequencing for comparing two different disease states
... We are thinking about designing an experiment comparing disease profiles of individuals belonging to two different disease states, the idea would be compare gene expression profiles from using T-cells. Since the goal is comparison of gene expression profiles, what platform would you recommended for ...
single cell rna-seq written 11 months ago by halo22120 • updated 11 months ago by igor7.7k
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Appropriate DESeq2 design for multi-factor comparison within group?
... Hello All, I am trying to run DE analysis using DESeq2 and wanted to know what would be a better/correct design matrix for my analysis. I have two disease condition A and B. Cells(CD4) from patient groups A and B were treated with different concentration of a certain chemical. The concentrations ar ...
deseq2 rna-seq written 19 months ago by halo22120 • updated 19 months ago by swbarnes25.8k
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Comment: C: Enrichr analysis using ranked gene list
... Great. Thank you very much. ...
written 20 months ago by halo22120
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Comment: C: Enrichr analysis using ranked gene list
... Thank you Santosh. I do have one more questions for you. What does the old.P.value in the enrichR output mean? How is it different from P.value. I am doing a KEGG analysis using enrichR. ...
written 20 months ago by halo22120

Latest awards to halo22

Popular Question 9 months ago, created a question with more than 1,000 views. For What is Digital Gene Expression?
Popular Question 14 months ago, created a question with more than 1,000 views. For Integrating WGS and RNA-seq data
Popular Question 14 months ago, created a question with more than 1,000 views. For What is Digital Gene Expression?
Popular Question 14 months ago, created a question with more than 1,000 views. For Single cell RNA sequencing with Fluidigm vs Drop-seq?
Popular Question 20 months ago, created a question with more than 1,000 views. For Single cell RNA sequencing with Fluidigm vs Drop-seq?
Popular Question 23 months ago, created a question with more than 1,000 views. For What is Digital Gene Expression?
Popular Question 7.2 years ago, created a question with more than 1,000 views. For How To Parse Data From An Owl File
Autobiographer 7.2 years ago, has more than 80 characters in the information field of the user's profile.

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