User: aranyak111

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aranyak1110
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Posts by aranyak111

<prev • 18 results • page 1 of 2 • next >
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Comment: A: PCA plotting using DESEq2 pipeline
... Using this option I found the following results. PC1 PC2 group condition name KDR1 -6.698822 2.27079850 wt wt KDR1 KDR2 -6.951940 -1.05877286 wt wt KDR2 KDR3 -6.951940 -1.05877286 wt wt KDR3 let7-1 7.320111 1.14917 ...
written 11 hours ago by aranyak1110 • updated 11 hours ago by GenoMax96k
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Comment: C: PCA plotting using DESEq2 pipeline
... where should I incorporate the returnData=TRUE in the code block? I have provided the whole code block to give the complete perspective. ...
written 18 hours ago by aranyak1110
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PCA plotting using DESEq2 pipeline
... I am working with 6 RNA libraries known as KDR1, KDR2, KDR3 wild-type zebrafish embryos, and three mutant embryos let71,let72,let7-3 mi -RNA mutant zebrafish embryos. I am using the DEseq2 pipeline for differential gene expressions. When I am trying to plot the PCA results I am getting only 5 dat ...
rna-seq written 18 hours ago by aranyak1110
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Comment: C: Heatmap of top 20 genes
... I want to make the heatmap of the top 20 genes but instead of having Ensembl gene ids in the heatmap. I want to label the heatmap with the genename. The code to generate the heatmap is as follows. How to go about it? ...
written 14 days ago by aranyak1110
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Heatmap of top 20 genes
... I am working with a zebrafish dataset with the following columns. geneid baseMean log2FoldChange lfcSE stat pvalue padj mir99-1 mir99-2 mir99-3 KDR1 KDR2 KDR3 genename ENSDARG00000087345 568.9632183 -6.20E+00 2.53E-01 -24.52506073 7.98E-133 1.39E-128 1184.991259 1155.817701 1040.461126 11.8 ...
rna-seq written 14 days ago by aranyak1110 • updated 14 days ago by Ram32k
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Comment: C: fastqc report and quality check
... ![enter image description here][1] https://ibb.co/Lvs51mF ...
written 16 days ago by aranyak1110
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Comment: A: fastqc report and quality check
... Please let me know if you can see the uploaded image and subsequently give your valuable opinion. [1]: http://%3Ca%20href=%22https://ibb.co/7ShFpQL%22%3E%3Cimg%20src=%22https://i.ibb.co/7ShFpQL/KDR1-fastq-Fast-QC-Report.jpg%22%20alt=%22KDR1-fastq-Fast-QC-Report%22%20border=%220%22%20/%3E%3C/a%3E ...
written 16 days ago by aranyak1110
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Comment: A: fastqc report and quality check
... [enter link description here][1] [1]: http://file:///C:/Users/Lenovo/DOCUME~1/MobaXterm/slash/RemoteFiles/395372_4_2/KDR1_fastqc.html.Let me know if you can access the link. ...
written 16 days ago by aranyak1110
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fastqc report and quality check
... I am conducting an RNA seq analysis pipeline for which I have to conduct fastqc report check. I am curious to know what is the exact significance of the parameter of the term per tile sequence quality. If this parameter seems problematic and other quality checks are okay can we still proceed with th ...
rna seq written 16 days ago by aranyak1110
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Volcano plot of Deseq2 data
... I am trying to generate a series of volcano plots of differentially expressed genes. The code snippet I am using is based on https://biocorecrg.github.io/CRG_RIntroduction/volcano-plots.html. The exact code I am using is data <- read.delim("E:/KDR-mir150 12.02.2021/KDR150diff.txt") ...
rna-seq written 19 days ago by aranyak1110

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