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Teichlab
BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
Bumps [idna](https://github.com/kjd/idna) from 3.4 to 3.7. Release notes Sourced from idna's releases. v3.7 What's Changed Fix issue where specially crafted inputs to encode() could take exceptionally long amount of time...
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Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.0.1 to 10.3.0. Release notes Sourced from pillow's releases. 10.3.0 https://pillow.readthedocs.io/en/stable/releasenotes/10.3.0.html Changes CVE-2024-28219: Use strncpy to avoid buffer overflow #7928 [@hugovk] Use functools.lru_cache for hopper() #7912 [@hugovk]...
Bumps [pycryptodome](https://github.com/Legrandin/pycryptodome) from 3.18.0 to 3.19.1. Release notes Sourced from pycryptodome's releases. v3.19.1 - Zeil Resolved issues Fixed a side-channel leakage with OAEP decryption that could be exploited to carry...
Bumps [fonttools](https://github.com/fonttools/fonttools) from 4.40.0 to 4.43.0. Release notes Sourced from fonttools's releases. 4.43.0 [subset] Set up lxml XMLParser(resolve_entities=False) when parsing OT-SVG documents to prevent XML External Entity (XXE) attacks (9f61271dc):...
Bumps [cryptography](https://github.com/pyca/cryptography) from 41.0.6 to 42.0.4. Changelog Sourced from cryptography's changelog. 42.0.4 - 2024-02-20 * Fixed a null-pointer-dereference and segfault that could occur when creating a PKCS#12 bundle. Credit to...
Hi I tried running BraCer on my Mac using docker, here is my command: `docker run -it --rm -v $PWD:/scratch -w /scratch teichlab/bracer test -o test_data` However, I got the...
Hi! I want to perform `run_IgBlast_IMGT_gaps_for_cell` in TCR data. Because Bracer summarise output is more abundant than Tracer. What do you think of its viability? Besides, I'd like to ask...
Hi, quick question: the **IGHDM** subtype indicates that both the IGHM and IGHD constant chain were mapped for that particular reconstructed BCR? So the cell contains the reconstructed heavy chain...
Bowtie2 seems to return very low VDJ alignment rates for each of my B cells and virtually no VDJ sequences were able to be reconstructed (BCR_summary.txt screenshot linked below). Because...
When I ran the latest docker container on test fastq data it crashes with IgBLAST subprocess [stdout.txt](https://github.com/Teichlab/bracer/files/4531788/stdout.txt) [stderr.txt](https://github.com/Teichlab/bracer/files/4531789/stderr.txt) Here is the command that was run: ``` bracer assemble --ncores 28...
