User: bharata1803

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bharata1803230
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Posts by bharata1803

<prev • 188 results • page 1 of 19 • next >
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Comment: C: GDC TCGA Metadata no project ID available?
... This is the metadata that I downloaded manually from GDC and then use my own parser: [csv file][1] [1]: https://www.dropbox.com/s/kjkfy9h6j2f6a9y/metadata_gbm.csv?dl=0 ...
written 6 days ago by bharata1803230
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Comment: C: GDC TCGA Metadata no project ID available?
... I see. If it is from GDC, maybe you can compare if you download manually from the portal. You can see whether the project_id exists in the original json format or not, if you still curious though. ...
written 6 days ago by bharata1803230
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Comment: C: GDC TCGA Metadata no project ID available?
... Have you downloaded metadata from the GDC website itself? It is in the json format. ...
written 6 days ago by bharata1803230
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Comment: C: GDC data only cancer sample without normal sample
... Thank you. I have solved this problem. From the new GDC portal, when we have selected all samples that we want to download, we can go to the download cart. From the download cart, we can download the samples metadata. The metadata contains a lot of information about each sample in json format. One o ...
written 6 days ago by bharata1803230
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Comment: C: Getting interesting gene ontology analysis result
... I also use cancer log fold change in the network to filter the nodes. My network now is a differentially expressed transcription factor network. Given nodes that are connected (subnetwork), I want to see what are the ontologies that are involved in that subnetwork and because all the nodes are diff ...
written 12 days ago by bharata1803230
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Comment: C: Getting interesting gene ontology analysis result
... So, what I've done is to create transcription factor network. What I do is I find target gene of a transcription factor that is also transcription factor. From this, I have a network of Transcription factors. You can imagine a chain of transcription factor that regulates each other. TF A regulates T ...
written 12 days ago by bharata1803230
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Getting interesting gene ontology analysis result
... I want to ask about gene ontology analysis. So, I have around 1,200 transcription factor genes ID (EnsEMBL id). I have done some clustering on a different constraint and I want to see the result of my cluster in the GO context. The only problem here is because all of them transcription factor, I al ...
ensembl go written 13 days ago by bharata1803230 • updated 12 days ago by Sean Davis23k
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Comment: C: Sample clustering from TCGA dataset
... thank you for your suggestion. ...
written 26 days ago by bharata1803230
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Comment: C: Sample clustering from TCGA dataset
... 1. I use |0.65| threshold for significantly up/down regulated. I agree that larger number of samples will give stronger statistical result but in this case, I am wondering whether there are variation in the tumor gene expression profile that make analysis for some genes don't give a strong result. ...
written 26 days ago by bharata1803230
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Sample clustering from TCGA dataset
... Hello all, I want to ask for your opinion. First of all I will explain my problem. I have around ~1000 genes of interest and all of them are transcription factor. I want to see the expression profile and do diff. exp. analysis between cancer-normal. I downloaded all TCGA BRCA dataset from GDC. I go ...
deseq2 rna-seq written 26 days ago by bharata1803230 • updated 26 days ago by Jean-Karim Heriche13k

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