Rachel Ng

Making yaml front matter persist

2

I want to use yaml frontmatter for general metadata of my notes (ex. status tracking). It has to be placed at the beginning of the markdown file according to Obsidian...

Hi, in the filtered fusions.fasta output run on a single sample, I found that the number of headers is larger than the number of unique sequences: ``` grep -v '>'...

Controlling error rate of substring within regular adapter

1

Is there a way to specify error tolerance for a specific subsequence within an adapter? For example, in my regular 5' adapter, the first 8 nucleotides indicates the sample identity...

Demultiplexing single-end reads with combinatorial dual indexes

3

cutadapt 4.2 with Python 3.10.9 Attempted to demultiplex nanopore single-end reads with combinatorial dual indexes, but it didn't work and created a file called `{name1}-{name2}.fastq.gz` `cutadapt -g file:barcodes_i5.fasta -a file:barcodes_i7.fasta...

Enable `gene_symbols` argument in mu.pl.embedding

1

**Is your feature request related to a problem? Please describe.** `sc.pl.embedding` takes an arugument `gene_symbols` that specifies which column in adata.var to look for the color keys. This argument does...

IEDB database cdr3_aa stored as junction_aa

10

**Describe the bug** IEDB database provides cdr3_aa sequences instead of junction_aa sequences. scirpy database import code puts this in the slot for junction_aa. The sequence would then be missing the...

Memory overload for large number of patients

3

I am trying to demultiplex 8000 cells that pooled 63 patients together using the following: ``` vireo -t GT -N 63 \ --vartrixData=${VARDIR}/vt_alt.mtx,${VARDIR}/vt_ref.mtx,${BC},${VCF} \ -d ${VCF} -o $OUTDIR ``` but...

Selective read/write mudata modalities

1

**Is your feature request related to a problem? Please describe.** Reading and writing MuData is a bit slow sometimes. For example, after doing some TCR sequence analyses the MuData takes...

Adding modality to MuData.mod

1

**Is your feature request related to a problem? Please describe.** After loading a CITE-seq 10x h5 file with muon and 10x vdj file with scirpy, I tried adding the AIRR...

Missing annot when using composite

1

**Describe the bug** Missing custom annot (stars indicating statistical significance) when using clustermap.composite. Individual `ClusterMapPlotter` calls successfully displayed the heatmap annotation. **Environment** Python 3.11.7 PyComplexHeatmap 1.6.4 matplotlib 3.7.1