User: star

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star240
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Posts by star

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Comment: C: Calculate p-value from Weibull distribution?
... Thanks for your reply. My data set is a kind of HiC data that shows the interaction between genomic regions. I would like to find the probability of observation which has stronger interaction under the Weibull distribution. So the hypothesis is like: if x refers to background and X refers to obser ...
written 9 days ago by star240
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Comment: C: Calculate p-value from Weibull distribution?
... Many thanks for your reply. but for finding p-value shall I consider the value of the function itself or do 1- pweibull()? ...
written 10 days ago by star240
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Calculate p-value from Weibull distribution?
... In the foloww up of my previous question` https://www.biostars.org/p/451743/#452019`. I have fitted a set of data into Weibull distribution and extract related parameters. Also, I have another set of data that I would like to calculate the p-value for each given value under the distribution. I calc ...
p-value statistic written 10 days ago by star240
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How to calculate probability of a value under Weibull distribution?
... I have fitted in R a Weibull distribution to my data like PD = fitdist(data,'Weibull'). Now I have a data point (e.g. x = 5) and I would like to calculate its probability under distribution. How can I calculate the probability (like a p-value)? Thanks in advance for any help! ...
genome R hic statistics written 11 days ago by star240
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Deconvolution RNA-seq based on Single-RNA-seq?
... I have bulk RNAseq expression data from heterogeneous samples (with different cell types). I would like to estimate the cell type proportions in each sample using the cell markers. There is a new publication on bioRxiv (https://www.biorxiv.org/content/10.1101/2020.01.10.897116v1) comparing differe ...
genome single-cell rna-seq written 5 weeks ago by star240
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Find interaction regions from HiC contact matrix?
... I downloaded a HiC normalized contact matrix like below (a subset of dig table). it is based on a 10kb resolution. The rows and columns should be the genomic coordinates based on 10000bp interval (e.g: Chr 18 length is 78,022,248 bp and the dimension of Chr 18 contact matrix is 7803*7803). df_ ...
gene R 4c hic chromosome_interaction written 6 weeks ago by star240
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Read subgroup of HDF5 file with (0,0) group name?
... I have an hdf5 file that I would like to read the subgroup of it. the file 'GSE77565_FBD_IC-heatmap-chr-10k.hdf5.gz' is downloaded from GEO number= 'GSE77565' I read the data like below: library(rhdf5) h5f = H5Fopen("file.hdf5") h5f HDF5 FILE name / file ...
rhdf5 python hdf5 dataframe pandas written 7 weeks ago by star240
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is there any difference between size of RefGenome in UCSC and Ensembl?
... I have downloaded the Human Refrence Genome from Ensembl and UCSC like below: UCSC: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz Ensembl: ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz and when I make the uncompressed using ...
ensembl alignment genome_build assembly ucsc written 3 months ago by star240 • updated 3 months ago by genomax87k
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Kruskal Wallis test with the same p-value for all data?
... I have a table like below. I calculated the Kruskal Wallis test on it to find the difference between time points, but I observed the same p-value for all rows. I would like to know is it normal or there is something wrong? set: coordinate T1 T2 T3 1:12740 ...
R non-parametric statistic kruskal-wallis written 5 months ago by star240 • updated 5 months ago by i.sudbery8.4k
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Comment: C: Repeated Measure ANOVA, GLM,GEE, Linear mixed model, Generalized linear mixed mo
... Thank for the reply! Do you mean that I consider each time point as an independent sample and apply comparison? but does it work when I don't have any replicate? ...
written 6 months ago by star240

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