User: pixie@bioinfo

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pixie@bioinfo1.4k
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Université Paris, Saclay
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PhD Student

Posts by pixie@bioinfo

<prev • 215 results • page 1 of 22 • next >
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CUT&RUN analysis pipeline
... Hello, My lab has generated data using the CUT&RUN protocol. Unfortunately, Its single-end data. I tried the CUT&RUN tools and the henipipe tool. Both are for paired end data. Any suggestion how I can analyse these data ? Any idea how to set the parameters in case I use the classical Trim ...
alignment sequencing written 5 days ago by pixie@bioinfo1.4k • updated 5 days ago by rpolicastro2.0k
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Bedtools to make a bed file for promoter
... Hello, I am trying to extract promoter locations based on the command: bedtools flank -i A.txt -g SLy4_genome.size -l 2000 -r 0 -s However, I am not getting any output. Sample files given below Kindly help. Thanks cat A.txt Chr0 93750 94430 Solyc00g500001 + Chr0 305442 306257 Solyc00 ...
bedtools written 15 days ago by pixie@bioinfo1.4k • updated 15 days ago by seidel7.1k
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DMR detection tools for whole genome bisulphite sequencing data in Plants
... Hello, I am working on whole genome methylation data in a plant. I am mostly looking for differential CHH and CHG marks. I tried MethylKit. I was looking for some more options on this. Thanks ...
R written 5 weeks ago by pixie@bioinfo1.4k • updated 5 weeks ago by Gautier Richard340
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Bismark: bedgraph to bigwig for DNA methylation
... Hello, I have a small question. I want to convert the bismark coverage files to bigWig format. I have the sample_CHG.gz.bismark.cov files. Other than the first 3 columns which refer to the chromosome and coordinates, which of the last 3 columns I should keep as the score for the bedgraph ? Thanks. ...
methylation written 5 weeks ago by pixie@bioinfo1.4k
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Forum: MOOC for AI and Machine learning for Bioinformatics
... Hello, I have decided to do some courses on AI and Machine learning. My long term goal is to use ML for omics data analysis. A search in google resulted in a large number of courses and I am not really sure which to go for, given that I do not get much time outside my lab hours. I have the basics ...
ai/ml forum written 9 weeks ago by pixie@bioinfo1.4k • updated 5 weeks ago by pradumnpc10
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Plant orthologous genes
... Hello, I have a list of gene IDs from rice. I want to have the orthologous genes in Arabidopsis, maize , wheat etc. Can someone suggest a database from which I can bulk download ? I wish to have the ortholog information for all genes in rice. Any suggestion is greatly appreciated ...
gene written 9 weeks ago by pixie@bioinfo1.4k • updated 9 weeks ago by lieven.sterck8.7k
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Comment: C: p value for permutation test for gene-interaction data
... Thats great, Merci beaucoup! ...
written 3 months ago by pixie@bioinfo1.4k
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p value for permutation test for gene-interaction data
... Hello, I have a data for pair-wise interactions between genes. I have taken the top 1000 interactions (ordered based on some value) and found that X no. of interactions in which Gene_1 is hypo methylated and Gene_2 is Up-regulated. My objective is to prove that the X no. of interactions (in the ord ...
statistics written 3 months ago by pixie@bioinfo1.4k • updated 3 months ago by Nicolas Rosewick9.2k
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Answer: A: How to combine two networks
... If they are in the form of edge-lists, you can append the two edge lists one after another and make a common edgelist. Then load it in Cytoscape and there is an option to remove duplicate edges. Don"t forget to add node and/or edge attributes to know which gene/edge is unique or common. Based on thi ...
written 4 months ago by pixie@bioinfo1.4k
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Statistical test for overlap
... Hello, I have a venn diagram with a list of up and down-regulated genes from experiment 1. I compared another gene list (from experiment 2) and got the overlap (108 genes are Up, 309 genes are Down and 41 genes are not deferentially expressed). My NULL hypothesis is that the proportion of overlaps ...
statistics written 4 months ago by pixie@bioinfo1.4k • updated 4 months ago by H.Hasani970

Latest awards to pixie@bioinfo

Great Question 19 days ago, created a question with more than 5,000 views. For Sequence Based Protein Interaction Information
Popular Question 6 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Epic Question 6 months ago, created a question with more than 10,000 views. For Coloring Multiple Nodes In Cytoscape
Great Question 8 months ago, created a question with more than 5,000 views. For T Cell Specific Gene Expression Data
Popular Question 14 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Great Question 14 months ago, created a question with more than 5,000 views. For T Cell Specific Gene Expression Data
Popular Question 14 months ago, created a question with more than 1,000 views. For KEGGREST: restricting pathways of compounds to certain organisms
Popular Question 14 months ago, created a question with more than 1,000 views. For How to start off building a Cytoscape plugin
Popular Question 14 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 18 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Appreciated 18 months ago, created a post with more than 5 votes. For T Cell Specific Gene Expression Data
Popular Question 18 months ago, created a question with more than 1,000 views. For KEGGREST: restricting pathways of compounds to certain organisms
Good Question 18 months ago, asked a question that was upvoted at least 5 times. For Disease Associated Snps
Student 18 months ago, asked a question with at least 3 up-votes. For Suggestions regarding bioinformatics journal
Popular Question 19 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Epic Question 20 months ago, created a question with more than 10,000 views. For Coloring Multiple Nodes In Cytoscape
Appreciated 20 months ago, created a post with more than 5 votes. For T Cell Specific Gene Expression Data
Great Question 22 months ago, created a question with more than 5,000 views. For T Cell Specific Gene Expression Data
Popular Question 22 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 23 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 2.0 years ago, created a question with more than 1,000 views. For KEGGREST: restricting pathways of compounds to certain organisms
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays

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