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#27 calls for splines (R built-in method smooth.spline) and lowess to be added
#49 calls for Savitzky-Golay to be added (which may simply be a general case of loess?)
#88 calls for better clarificat…
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**Question**
In chapter [Integrating AIR and transcriptomics](https://www.sc-best-practices.org/air_repertoire/multimodal_integration.html), the recommended integration is using function `scirpy.pp.m…
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1. mds_tokyo_2011
https://cbioportal.mskcc.org/study.do?cancer_study_id=mds_tokyo_2011#summary
2. lcll_icgc_2011
https://cbioportal.mskcc.org/study.do?cancer_study_id=lcll_icgc_2011#summary
3. a…
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## Is your feature request related to a problem? Please describe
TRUST4 claims they can call TCRs not only from VDJ-enriched 10x data, but also regular 10x 5' seq and other scRNA-seq protocols.…
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Hi Heng,
I notice a path `>s48420>s48421>s48428` in the `--call` outputs that doesn't actually exist in the `GRCh38-freeze1.gfa` because there is no such link between `s48421` and `s48428`.
Here a…
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Based on the [MAESTRO paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02116-x#Sec12), my understanding is that a peak that is in the exons or promoter region of more than on…
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https://www.nature.com/articles/s41467-020-20887-6
- [ ] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this c…
jjgao updated
2 years ago
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Hello,
I have attempted to use TRUST4 to assemble my SE RNAseq data and have learned the basics of how it works. However, I am still confused about the final report.
In the .report file, I notic…
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Ciao !
On a fresh MAESTRO — release 1.5.1 — installation (Ubuntu 18.04 with Python v3.8.12 installed) I tried to run `chromap`, `chromap --version` or `chromap -h` having immediately `Illegal instruc…
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Hello,
I am using TRUST4 on my RNAseq data to reconstruct BCR sequences. Since I am specifically interested in clonal reconstruction, sequence_id guides me on number and sizes of clonal groups (to be…