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I have read your paper, but there is a problem that I don't quite understand. The p value of genes is estimated by the p value of transcript difference analysis, and basemean in transcript difference …
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I download the pre-trained model from https://maayanlab.cloud/sigcom-lincs/#/Download
I found L1000_to_RNAseq_pipeline_training.ipynb said the input is Level 3 of L1000.
I used the DeepCE model…
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Hello,
I was wondering if you can help me with the following error? Thank you!
I am using the BigPint pipeline on my own RNAseq data. Everything works up until this point, I can create the paralle…
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Hi, I am using cromwell-59.jar, and run in local backend mode.
Used command:
`java -Dconfig.file=cromwell.examples.conf -jar ~/softwares/cromwell-59.jar run example.wdl -i input_detail.json`
ho…
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Once we have CI setup, we'll be pushing this project to PyPi and will want an up-to-date README.
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Here's a few things that could be shared across our RNA-Seq pipelines:
- fetching FASTQ data from GEO/SRA and ArrayExpress
- building STAR index and various references
- alignment
- quality …
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Hey guys, thanks for the tool! Very useful!
I'm a bit confused about the "num_reps" parameter. And also who it relates to the event probabilities.
I have implemented an alternative splicing (AS)…
ls233 updated
8 months ago
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I'm wondering if there is concise documentation somewhere for reproducing the exact analysis of the TCGA/GTEX data in this [paper](https://www.nature.com/articles/nbt.3772) (but with new samples).
h…
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I have been trying to use align_and_estimate_abundance.pl script, with bowtie2 and bowtie, but get similar errors. Could you please help with revolving the issue?
----- bowtie2 --------
align_and…
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I'm trying to get this running on Google Cloud Platform using [https://github.com/broadinstitute/wdl-runner](url)
Unfortunately, the outputDir is pervasive throughout the WDL files and seems to be a …