User: ChIP

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ChIP500
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Posts by ChIP

<prev • 101 results • page 1 of 11 • next >
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Comment: C: Matplotlib comprehensive chromosome drawing
... @ Ryan Dale: How can I add multiple peak sets? I guess the one here is for one peak set. Could you please highlight that part or adjust the script that it works for more than one peakset. ...
written 17 days ago by ChIP500
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Comment: C: Best input sample (CNV)
... They have it, the point is should I use individual inputs or should I merge them all and use it. ...
written 20 months ago by ChIP500
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Comment: C: Best input sample (CNV)
... Hi, Yes, I meant copy number alterations or structural variants, as in, for example, changes between a germline DNA sample and that of a tumour that has a high level of genomic instability. ...
written 20 months ago by ChIP500
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Best input sample (CNV)
... Dear All, I have 3 input samples, and I want to compare them and find out which is the best input to be used for peak calling. These samples have copy number variation. Any help is appreciated. ...
chip-seq written 20 months ago by ChIP500
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Downloading genomic interval for hg38
... Hi, I want to download genomic information for hg38, that have following information: region gene exon/tss/intron/intergenic/CpG/nonCpG The idea is to get this in a table format and then use intersectBed to to get overlap between the ChIP-seq data and this genomic information file. How can I get ...
chip-seq written 2.0 years ago by ChIP500 • updated 2.0 years ago by Alex Reynolds28k
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Comment: C: Binning the genomic regions and counting reads
... Hi, Thank you for your answer, I have an additional question. How can I plot these numbers as an heatmap or average coverage profile. Thank you ...
written 2.3 years ago by ChIP500
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Binning the genomic regions and counting reads
... Hi, I have list of genomic regions: chr14 83053041 83062424 chr4 9160067 9223997 chr2 144458153 144467912 chr10 86819472 86833402 chr12 39614733 39641285 chr4 68608137 68629925 chr17 36334147 36408831 chr12 19306607 19314016 chr4 97531083 97537086 chr2 88351 ...
bed tool bash written 2.3 years ago by ChIP500 • updated 2.3 years ago by James Ashmore2.6k
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Identifying DEG from time course data without condition
... Hi, I have a a time course data for 7 time points with 3 replicates each and I would like to point out the clusters of genes that are differentially expressed in at least one group Vs others. Similar problems with control and treatment problems can be solved with DESeq2 but I don't have 2 conditio ...
deseq edger rna-seq written 2.6 years ago by ChIP500 • updated 2.6 years ago by Benn7.1k
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User guide of FunPat
... Hi, Could anyone of you share the user guide for FunPat. Unfortunately I couldn't find it on internet. Thank you ...
funpat written 2.7 years ago by ChIP500
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Comment: C: Ensembl ID conversion for a specific build
... Thank you so much. The information and the link was very helpful. ...
written 2.7 years ago by ChIP500

Latest awards to ChIP

Great Question 18 months ago, created a question with more than 5,000 views. For Trimming read length & quality in a FASTQ file
Great Question 18 months ago, created a question with more than 5,000 views. For Hypergeometric Test On Gene Set
Popular Question 18 months ago, created a question with more than 1,000 views. For SNP zygosity from RNA-Seq data (BAM file)
Great Question 18 months ago, created a question with more than 5,000 views. For Copy Number Variation from paired end RNA-Seq data
Popular Question 18 months ago, created a question with more than 1,000 views. For Heatmap of Differentially Expressed Genes
Great Question 18 months ago, created a question with more than 5,000 views. For Heatmap In R With Large Datasets
Popular Question 18 months ago, created a question with more than 1,000 views. For Converting Solexa eland to Solexa fastq
Epic Question 18 months ago, created a question with more than 10,000 views. For Hypergeometric Test On Gene Set
Popular Question 18 months ago, created a question with more than 1,000 views. For Difference between the PFam domain information from UCSC and PDB site
Epic Question 18 months ago, created a question with more than 10,000 views. For GT and GL fields in VCF file
Popular Question 19 months ago, created a question with more than 1,000 views. For Heatmap of Differentially Expressed Genes
Epic Question 19 months ago, created a question with more than 10,000 views. For Hypergeometric Test On Gene Set
Centurion 20 months ago, created 100 posts.
Popular Question 23 months ago, created a question with more than 1,000 views. For SNP zygosity from RNA-Seq data (BAM file)
Popular Question 23 months ago, created a question with more than 1,000 views. For Heatmap of Differentially Expressed Genes
Popular Question 23 months ago, created a question with more than 1,000 views. For Copy Number Variation from paired end RNA-Seq data
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Heatmap In R With Large Datasets
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Heatmap In R With Large Datasets
Good Question 2.3 years ago, asked a question that was upvoted at least 5 times. For Plotting Reads Around Tss
Great Question 2.3 years ago, created a question with more than 5,000 views. For Heatmap In R With Large Datasets
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Hypergeometric Test On Gene Set
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Normalizing Bam Files
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Heatmap In R With Large Datasets
Great Question 2.5 years ago, created a question with more than 5,000 views. For Heatmap In R With Large Datasets

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