Jiayi-Zheng
Jiayi-Zheng
Hello, I was trying to analyze a 10X data. I wanted to see the manual of bam2vcf.py by `python bam2vcf.py --help` However, it returns error: ``` File "bam2vcf.py", line 3,...
Hi, I was using command `seqtk subseq uniprot_sprot.fasta name.txt > out.fa` my name.txt looks like: ``` sp|Q9H2Y7|ZN106_HUMAN Zinc finger protein 106 OS=Homo sapiens OX=9606 GN=ZNF106 PE=1 SV=1 sp|Q9Y5V0|ZN706_HUMAN Zinc finger...
Hello, I was working step-by-step with `https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_SCENIC-protocol-CLI.ipynb` During `STEP 2-3: Regulon prediction aka cisTarget from CLI`, I did: ``` import glob # ranking databases f_db_glob = "/gene_based/*feather" f_db_names = '...
Hello, I had a lot of problem installing seurat 5 so i ended up retorting to installing seurat 4. However, the new seurat-wrappers can only fit seurat 5. I couldn't...
Hello, I was trying AUCell with R and: ``` > library(AUCell) > cells_AUC ls("package:AUCell") [1] "AUCell_buildRankings" "AUCell_calcAUC" "AUCell_createViewerApp" "AUCell_exploreThresholds" "AUCell_plotHist" [6] "AUCell_plotTSNE" "aucellResults" "cbind" "getAssignments" "getAUC" [11] "getRanking" "getSetNames" "getThresholdSelected"...
On conda installation page it says `conda create -n scenic_protocol python=3.6` however when doing `pip install pyscenic` it tells me no available pandas1.3.5, and according to pandas their 1.3.5 is...
Sorry this is a very naive question but I couldn't seem to find the answer. I was analysing a spatial seq dataset whose pca explains very limited variance. So I...
Hello, I'm using stereo-seq with lower bin size, and so I've got a few ten thousands of pixels, when I try to run spatialdm_local it tells me my memory is...
Hello, the package was running smoothly when I use all default setting. Until I checked the manual of create.RCTD hoping to adjust arguments for better model fitting. I saw that...