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Hi,
I would like to use TRUP to detect chimeric fusions in my RNA-Seq datasets. Unfortunately, I keep running into the following issue:
# RTrace.pl --runlevel 4 --sampleName sample --seqType p --read…
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## RNA-seq from loterature
- [x] `BAM` to `bigWig`
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Credits to Katie Hoadley, who would be interested in using this on a dataset of hers
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Hi,
I have a question on cell type proportion estimates. I have a single cell RNA-seq reference data like the below toy example,
Genes CD4 Mono Ery
ACE 49 1 0
ALG9 401 74 234
ANKRD18…
Jia21 updated
4 years ago
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Step to reproduce:
1. Go to SCXA home page and click on `CFTR` link from the list of examples
**Expected result:**
In the resulting table the `Number of assays` should be populated of the number of…
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Reported by @anjaf who can maybe point to some examples. Maybe an issue in the jq filtering calls?
pcm32 updated
2 years ago
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Hi Onur,
This is a fascinating study on the deconvolution of bulk RNA-seq in AML. I am a postdoctoral researcher at the Chinese Institutes for Medical Research (CIMR).
Your code serves …
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- Link to publication: https://www.biorxiv.org/content/10.1101/2021.06.04.447088v1
- Title of publication: Single-cell RNA-sequencing reveals widespread personalized, context-specific gene expression…
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Dear Meichen,
I am trying to run SCDC with only one reference single cell rna seq data set, i.e. only one subject, e.g. sample H2 in Segerstolpe example data set.
SCDC_prop_ONE() runs until it enc…
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I'm trying to create a function that extracts the necessary information directly from adata files
```
def annData_converter(
sc_adata, st_adata, sc_annotation="ann_level_3_transferred_label…