User: star

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star260
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Posts by star

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Comment: C: How to calculate number of fragment and its coverage from BAM file?
... Thanks, ATpoint. I have checked `genomecov` with -bg -pc and it is similar to `bamtobed` outputs. But I will go for `genomecov` as it sums up overlap regions : The output of bamtobed: 1 785101 785152 1 785152 785203 4 1 824806 824855 1 824932 824983 3 1 ...
written 9 days ago by star260
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How to calculate number of fragment and its coverage from BAM file?
... I have a bam file like, It is the Paired-End sequenced data with the length 50 bp. I would like to count the number of the fragment (e.g: chromosome,start-read1,end-read2) and its coverage. I have used `Bamtobed` and `Genomecoverage`, but I am confused about which one gives me the correct number. ...
genome bedtools alignment rna-seq written 9 days ago by star260
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How convert log2 value to raw value in R?
... I have a data table that I would like to run expression analysis on it but the data set is present in log2. I would like to know how can I get Raw value instead of log2? Data: in Log2 Gene_names G_rep1.Log2 G_rep2.Log2 G_rep3.Log2 ACTG1 ...
R written 8 weeks ago by star260
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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 12 weeks ago by star260
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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 12 weeks ago by star260
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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 3 months ago by star260
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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 3 months ago by star260
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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 3 months ago by star260
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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 4 months ago by star260
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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 4 months ago by star260

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