User: pixie@bioinfo

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pixie@bioinfo1.4k
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PhD Student

Posts by pixie@bioinfo

<prev • 207 results • page 1 of 21 • next >
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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 16 days ago by pixie@bioinfo1.4k
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5 follow
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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 18 days ago by pixie@bioinfo1.4k • updated 18 days ago by H.Hasani920
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Comment: C: Boxplots from ChIP-seq Data
... Thanks for the inputs. I ended up using deeptools and it worked fine. ...
written 3 months ago by pixie@bioinfo1.4k
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Boxplots from ChIP-seq Data
... Hello All, I have ChIP-seq bam files from two contrasting conditions. I have a bed file with a pre-defined list of chromosome positions. I wish to have the boxplots for the intensities for the predefined positions. How can I go about it ? Thanks ...
chip-seq written 3 months ago by pixie@bioinfo1.4k • updated 3 months ago by Friederike5.7k
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Heatmap using Interaction/HiCHip data
... Hello, I have two interaction files for two different stages S1 and S2 as obtained from HiCHip data and have analysed it. I have associated Gene annotations to the chromosome regions wherever possible. I want to plot contrasting interaction profiles which are lost/gained in the two stages, but not s ...
ngs heatmap written 4 months ago by pixie@bioinfo1.4k
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Job: Post-Doctoral position (Bioinformatics) in the Chromosome Dynamics team at the Institut des Sciences des Plantes - Paris-Saclay (IPS2)
... The Chromosome Dynamics Group is seeking a Post-Doc in Bioinformatics. Using experimental and computational approaches, our ambitious group has a broad interest in genome organization and its influence on gene regulation. We use molecular methods (Hi-C, ChIAPET, ChIP-seq, DNA- methylation analysis a ...
R next-gen chip-seq job written 4 months ago by pixie@bioinfo1.4k
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Finding over and under-represented interactions using HOMER
... I am analyzing Hi-C data with HOMER. My experimental set up is time-point wise analysis of stress (0,1 and 6 hrs). For a differential analysis, say 6 hrs vs 0 hr, how can I find interactions which are over-represented, under_represented and specific to only one condition ? I had initially just used ...
homer hic written 5 months ago by pixie@bioinfo1.4k
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KEGG pathway visualization AND Cytoscape
... Hello, I have been trying to visualize KEGG pathways for a group of metabolites (in Tomato). I am getting mappings to 34 different pathways, many of which have common metabolites. My supervisor wants me to combine the individual pathways in a global map so that we can color code the nodes and see th ...
kegg written 10 months ago by pixie@bioinfo1.4k • updated 10 months ago by sgoetz12320
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Comment: C: Intersecting regions in the genome
... Okay, Thanks I am looking into this ...
written 14 months ago by pixie@bioinfo1.4k
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Intersecting regions in the genome
... I had written a python code which outputs list of lists of start and end positions of chromosomal coordinates corresponding to certain GC% bins for example, `GC_10: [[20451, 20500], [32451, 32500], [38301, 38350]]` `GC_50: [[615051, 615100], [616501, 616550], [622201, 622250], [623301, 623350]]` ...
genome written 14 months ago by pixie@bioinfo1.4k

Latest awards to pixie@bioinfo

Popular Question 12 weeks ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Epic Question 12 weeks ago, created a question with more than 10,000 views. For Coloring Multiple Nodes In Cytoscape
Great Question 4 months ago, created a question with more than 5,000 views. For T Cell Specific Gene Expression Data
Popular Question 10 months ago, created a question with more than 1,000 views. For How to start off building a Cytoscape plugin
Popular Question 10 months ago, created a question with more than 1,000 views. For KEGGREST: restricting pathways of compounds to certain organisms
Great Question 10 months ago, created a question with more than 5,000 views. For T Cell Specific Gene Expression Data
Popular Question 10 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 10 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Appreciated 14 months ago, created a post with more than 5 votes. For T Cell Specific Gene Expression Data
Student 14 months ago, asked a question with at least 3 up-votes. For Suggestions regarding bioinformatics journal
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 Differential Gene Expression Analysis with NimbleGen microarrays
Good Question 14 months ago, asked a question that was upvoted at least 5 times. For Disease Associated Snps
Popular Question 15 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Epic Question 16 months ago, created a question with more than 10,000 views. For Coloring Multiple Nodes In Cytoscape
Appreciated 16 months ago, created a post with more than 5 votes. For T Cell Specific Gene Expression Data
Great Question 18 months ago, created a question with more than 5,000 views. For T Cell Specific Gene Expression Data
Popular Question 18 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 19 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 20 months ago, created a question with more than 1,000 views. For KEGGREST: restricting pathways of compounds to certain organisms
Popular Question 20 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 21 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 22 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
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 How to start off building a Cytoscape plugin

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