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Questions related from Wang Lu
The relationship between gene expression and disease was widely known, however, is the gene ratio (Gene A expression value/Gene B expression value) might cause any diseases or phenotypes in any...
22 June 2021 5,500 5 View
What is the best practice to perform LEFSe? In qiime2 or transforming qiime2 object into LEFse obejct? There is a tool. However, it easy to error. https://github.com/gblanchard4/qiime_to_lefse...
27 September 2019 6,734 3 View
Hi Thank for your attention.We are planing to develop a method to predict the occurrence for type 1 diabetes based on infant gut microbiota. To train the model , more datasets are needed....
18 August 2017 5,522 3 View
In gene regulatory network, we can always map the network we newly build, to a database like KEGG, to find the specific function of nodes. However, for a microbial network, which node is...
09 December 2016 8,333 2 View
I have build a gut microbiome network using public data, which just contain less than 100 species as nodes. And, when I sum species' relative abundance(relative abundance has already contained in...
17 August 2016 6,414 2 View
We found that at the same concentration of a medium-chain free fatty acid, it had a poor inhibitory effect on high concentrations of bacteria and a high inhibitory effect on low concentrations of...
01 January 1970 6,716 6 View
This feature correlated (cor = 0.4) with our target, however, lasso return no coefficient for any variable. Our code is like (sklearn) lassocv2 = LassoCV(cv =features.shape[0], random_state =...
01 January 1970 6,742 2 View
Sample size was well known to influence edge weight in correlation network. We plan to construct networks for A (n=152) and B (n=30) groups of samples (human gut microbiome). Do you think we...
01 January 1970 3,271 3 View
Our input data is a table of edges (potential edges) and a list of nodes.
01 January 1970 1,745 3 View
For example, I have known variables x and y have nonlinear relationships with the score, however the model of x, y to the score is unknown. We want to know which values of x and y can lead to the...
01 January 1970 507 3 View
Might integrate prior knowledge into error calculation will help to generate feature embedding. I am newbie to matrix decomposition, could you kindly suggest how to code it with R or python?
01 January 1970 1,206 4 View
The error rate of tensor (CP) decomposition returned by python module tensorly is 0.4 or 0.9, is it satisfying? What is your advice to decrease error in tensor (CP) decomposition or matrix...
01 January 1970 9,840 1 View
Is there a function that can directly remove mitochondrial genes. Thank you for your help!
01 January 1970 8,923 1 View
If input array is 2000*2000*3000 or larger, how can we decompose it with limited memory? Most packages on tensor decomposition or factor analysis method, were not suitable to deal with large array.
01 January 1970 7,421 1 View
We generated unsymmetric distance matrix which measure the similarity between samples. Could you recommend to a R or python function, or a custom code to perform permanova analysis?
01 January 1970 6,063 2 View
Add too much feature (less alpha) just make it overfit. However, bigger alpha make it underfit. We do not have more data and features, which way can improve?
01 January 1970 4,506 0 View
There are large files in NCBI, such as this, a 25GB file https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185948 I do know how to download it by cutting it with custom filters for smaller...
01 January 1970 6,220 4 View
How to download the KO (KEGG Orthology) Database, or list all pathways and their KEGG Orthology for 100 species. I known keggREST. However, bad request error appeared many times. Do you have a...
01 January 1970 3,514 2 View
For pure scATAC-seq dataset annotation, without any scRNAseq information, there are several popular pipelines. However, is there a pipeline with code for this?
01 January 1970 9,058 0 View
Python code: class HGNN(nn.Module): def __init__(self, H, in_size, out_size, hidden_dims=hidden_dim): super().__init__() self.Theta1 = nn.Linear(in_size, hidden_dims) self.Theta2 =...
01 January 1970 5,887 4 View
Is there a R or python package, can annotate the function or related disease of individual genes? Thank you for your attention.
01 January 1970 5,084 3 View
AnnotationDbi can annotate gene with its full name or GO term. However, how to annotate individual ligand-receptor pairs? For example, KNG1-BDKRB2, how can you annotate its role or function with...
01 January 1970 8,311 2 View
For example, The id of Adenocarcinoma is C0001418 https://www.ncbi.nlm.nih.gov/medgen/122. Is there a R function can transform it into KEGG disease ID, such as H00287?
01 January 1970 9,714 1 View
For example, we want to convert WP_217954729, into Alistipes timonensis, sulfatase. https://www.ncbi.nlm.nih.gov/protein/WP_217954729.1/ I do know it is easy for the convertion of human protein,...
01 January 1970 3,213 1 View
Our study have scRNA + scATAC sequencing on same sample, however, there are more than 40% mito (mitochondrial ) genes in about 50% cells. After repeat with different experiment methods, this...
01 January 1970 7,165 3 View
According to the formula of R-squared below (wiki), since I have only one predicted target value for each of the N folds, R2 is zero unless the predicted value coincides exactly with the true...
01 January 1970 4,909 3 View
Is there a tool on linux (server) that can stop/continue the transfer, download all addresses contained in a text, and be able to manually change the address to continue the download after the...
01 January 1970 362 7 View
The previous discussion can introduce the AU, BP P value to us. https://stackoverflow.com/questions/43576210/p-values-in-pvclust-results-in-hclust However, why there is zero in my top 2 levels...
01 January 1970 7,631 0 View
Now we have variables like diet (fiber, fat, and protein), exercise (vo2 max), the exact date of intervention (just before and after), BMI, and metabolite data. Our specific objective was to...
01 January 1970 8,018 0 View
In CP decomposition, how can we determine the component number for CP decomposition?
01 January 1970 6,733 2 View
It is a dta file, can not be read with read.csv. I used haven to read it. However, the second row of column is real name, such as Checking Year and Checking Month , how can you extract it?
01 January 1970 5,294 6 View
How can I export the pseudotime numbering in Monocle 3 and identify which nodes belong to a specific cluster, such as cluster 1 represented by a solid circle in the plot generated by...
01 January 1970 1,296 0 View
When install Alphafold2, the scripts (such as ./download_alphafold_params.sh) was seem to be necessary. It need aria2c. I tried to install with conda, and it can not be found and can not be...
01 January 1970 5,294 0 View
I need a specific tutorial on how to install alphafold-multimer on a server that I don't have permission to (I can use conda and can not use docker. I install cuda 11, the nvcc version shows cuda...
01 January 1970 8,590 1 View
For example: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:137113 Is there an API or package that can automatically download the Role Classification of a molecule?
01 January 1970 320 0 View
In 16s sequencing data, we found a few very interesting species as biomarkers, so our laboratory invested good money for metagenomics out of the desire for greater study. However, in...
01 January 1970 2,159 2 View
In the same study, fungi OTUs are analyzed by species, bacteria OTUs by genus. This is what the data looks like, and we can not re-analysis it. Does that make scientific sense and common in...
01 January 1970 3,793 2 View
cds
01 January 1970 2,078 0 View
How to download the KEGG pathways related to all diseases?
01 January 1970 8,696 2 View
For example, we known CE4, CE7, GH3, GH43, GH51 and GH115 are related to Arabinoxylan. However, how can we see if those are all arabinose related families ? Which tool you recommend to detect more...
01 January 1970 3,284 0 View
Spearman can relate Kegg and taxonomy based on their abundance tables. However, it is well known to generate spurious correlations. Could you recommend a better method?
01 January 1970 5,156 2 View
Our gut metagenomics samples has delete gene content related to human genome, however ,there is a large fraction of gene were mapped to human related pathway. How can I known, whether this caused...
01 January 1970 2,325 0 View
