diffxpy
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theislab
Differential expression analysis for single-cell RNA-seq data.
I was originally trying to use the `rank_genes_groups()` function in scanpy to get p-values and logfoldchanges between a single condition and a reference condition. My end-goal was to take the...
Hi I am trying to apply diffxpy to my data which has about 300 cells on rows and about 17k genes on columns. I have two predefined clusters. When I...
https://nbviewer.org/github/theislab/diffxpy_tutorials/tree/master/diffxpy_tutorials/enrich/enrich.ipynb/ 404: not found
I'm attempting to run rank_test() on subgroups in an AnnData object, by making use of test.partition(). There appears to be a syntax error, where in the rank_test method of a...
Hi, Thanks for developing this package! With the increasing throughput of single cell technology, a lot more samples (individuals in the context of human tissue) are being sequenced. The variation...
It'd be more accurate to replace "qval" with "fdr_bh", because q-value typically refers to Storey q-value AFAIK (https://projecteuclid.org/journals/annals-of-statistics/volume-31/issue-6/The-positive-false-discovery-rate--a-Bayesian-interpretation-and/10.1214/aos/1074290335.full).
I tried to run diffxpy with tf1 and normal noise. However, I get the below error. ``` import diffxpy.api as de from anndata import AnnData import pandas as pd import...
I was using `diffxpy` to find marker-genes for a cluster vs all other clusters in a scRNA-dataset stored in `adata`. When performing the following: ```python # Performing differential expression to...
Hey, ``` import diffxpy.api as de de_w_test = de.test.wald( data=leukocytes_only_raw.X, formula_loc="~ 1 + condition", factor_loc_totest="condition", gene_names=leukocytes_only_raw.var_names, sample_description=leukocytes_only_raw.obs, ) ``` results in ``` ╭──────────────────────────── Traceback (most recent call last) ────────────────────────────╮ │...
I tried to model a single gene across different cell types with diffxpy, but I get the below error. Today I switched to latest dev, but the same also happens...