User: pixie@bioinfo

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pixie@bioinfo1.4k
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PhD Student

Posts by pixie@bioinfo

<prev • 203 results • page 1 of 21 • next >
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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 21 days 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 21 days 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 7 weeks 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 6 months ago by pixie@bioinfo1.4k • updated 6 months ago by sgoetz12320
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Comment: C: Intersecting regions in the genome
... Okay, Thanks I am looking into this ...
written 10 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 10 months ago by pixie@bioinfo1.4k
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Comment: C: Unable to map genes to KEGG pathway using pathview
... Hi, could you solve your issue ? I am facing the same problem ...
written 10 months ago by pixie@bioinfo1.4k
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Ideas for integrating transcriptomic data/co-expression network and genome-scale metabolic networks
... Hello, I have RNA-seq time-series data from various stress conditions of a plant. I have the stress and time-point specific DEGs, as well as co-expression networks of the DEGs. I need some idea as to how I can use the genome-scale metabolic network (GEM) of the given plant for an integrated analysis ...
pathway rna-seq written 11 months ago by pixie@bioinfo1.4k
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Answer: A: How to get the pathway-protein relationship?
... You can try STRING DB. The give protein-protein interactions + KEGG pathway annotations ...
written 11 months ago by pixie@bioinfo1.4k
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Comment: C: Calculating correlations using data from different experimental methods for a co
... Correct, zero read counts for the given gene, so plug in RT-PCR data ...
written 11 months ago by pixie@bioinfo1.4k

Latest awards to pixie@bioinfo

Popular Question 5 months ago, created a question with more than 1,000 views. For How to start off building a Cytoscape plugin
Popular Question 5 months ago, created a question with more than 1,000 views. For KEGGREST: restricting pathways of compounds to certain organisms
Popular Question 5 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Great Question 5 months ago, created a question with more than 5,000 views. For T Cell Specific Gene Expression Data
Popular Question 6 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Good Question 10 months ago, asked a question that was upvoted at least 5 times. For Disease Associated Snps
Popular Question 10 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Appreciated 10 months ago, created a post with more than 5 votes. For T Cell Specific Gene Expression Data
Popular Question 10 months ago, created a question with more than 1,000 views. For KEGGREST: restricting pathways of compounds to certain organisms
Student 10 months ago, asked a question with at least 3 up-votes. For Suggestions regarding bioinformatics journal
Popular Question 11 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Appreciated 12 months ago, created a post with more than 5 votes. For T Cell Specific Gene Expression Data
Epic Question 12 months ago, created a question with more than 10,000 views. For Coloring Multiple Nodes In Cytoscape
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 15 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 16 months ago, created a question with more than 1,000 views. For Differential Gene Expression Analysis with NimbleGen microarrays
Popular Question 16 months ago, created a question with more than 1,000 views. For KEGGREST: restricting pathways of compounds to certain organisms
Popular Question 17 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
Popular Question 18 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 How to start off building a Cytoscape plugin
Popular Question 19 months ago, created a question with more than 1,000 views. For Internship opportunities for PhD students ?
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