User: Kamil

gravatar for Kamil
Kamil1.6k
Reputation:
1,650
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Location:
Boston
Website:
http://slowkow.com/
Twitter:
slowkow
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Google Scholar Page
Last seen:
1 day, 15 hours ago
Joined:
7 years, 3 months ago
Email:
k***********@gmail.com

Posts by Kamil

<prev • 95 results • page 1 of 10 • next >
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Comment: C: Tutorials for Library Normalization in DESeq2 and EdgeR
... Also check out Joshua Starmer's other great videos here: https://statquest.org He's done a fantastic job breaking down statistical ideas and explaining them step by step. ...
written 9 weeks ago by Kamil1.6k
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Comment: C: Produce PCA for 1000 Genomes Phase III in VCF format
... Looks nice! Thanks for posting. Could I ask you to please include a PCA figure directly in your post? ...
written 10 weeks ago by Kamil1.6k
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Comment: C: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
... My script expects to read a file compressed with `gzip`, but you provided a decompressed file. Try running `gzip gene2ensembl` and then run the script again. ...
written 10 months ago by Kamil1.6k
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Comment: C: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
... I updated the comment in `count_bp` with a visual example of how exons are counted. You can find gene annotations in GTF format for many species here: ftp://ftp.ensembl.org/pub/release-87/gtf/ Note that the version (87 at the time of this post) is continually updated over time. Regarding convert ...
written 10 months ago by Kamil1.6k
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Comment: C: Calculating TPM from featureCounts output
... Thanks for the suggestion! I [modified the function][1] for you. [1]: https://gist.github.com/slowkow/c6ab0348747f86e2748b#file-counts_to_tpm-r-L44 ...
written 12 months ago by Kamil1.6k
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Comment: C: RNA-seq: differentially expressed genes without genome reference
... Kallisto requires sequencing reads and a file with target sequences. Please see the [kallisto manual](https://pachterlab.github.io/kallisto/manual) for more information. ...
written 13 months ago by Kamil1.6k
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Answer: A: Download Transcription Factor Targeting Genes Data
... You might be interested in this R package: https://github.com/slowkow/tftargets It summarizes 6 datasets: * [TRED][tred] (2007) * [ITFP][itfp] (2008) * [ENCODE][encode] (2012) * [Neph2012][neph2012] (2012) * [TRRUST][trrust] (2015) * [Marbach2016][marbach2016] (2016) [tred]: https://github.com/sl ...
written 13 months ago by Kamil1.6k
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Answer: A: quantify signal in a chromosomal interval in different .bw files
... ## bigWigToBedGraph Download `bigWigToBedGraph` from: http://hgdownload.cse.ucsc.edu/admin/exe/ You can pass genomic coordinates like this: $ bigWigToBedGraph -chrom=chr1 -start=123 -end=456 input.bw output.bedGraph ## bwtool [Ming Tang](https://twitter.com/tangming2005/status/72515445552449 ...
written 19 months ago by Kamil1.6k
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Answer: A: RNA-seq: differentially expressed genes without genome reference
... If you know which transcripts belong to a gene, then you can sum their TPM values to get the gene's TPM. Consider using Kallisto to get quick and accurate results. Next, use your preferred method for differential expression analysis: limma, DESeq, edgeR, etc. ...
written 21 months ago by Kamil1.6k
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Answer: A: automated gene ontology enrichment for simple gene list (not microarray data)
... You might start by considering a function in the limma package called goana. See the examples in the documentation. The function can perform an enrichment test even if you only provide a vector or Entrez Gene IDs, without any other inputs. See all the other packages available for Gene Set Enrichmen ...
written 21 months ago by Kamil1.6k

Latest awards to Kamil

Appreciated 9 days ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Path
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Path
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Tutorials for Library Normalization in DESeq2 and EdgeR
Librarian 9 weeks ago, created a post with more than 10 bookmarks. For FASTA and FASTQ tools
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Path
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Path
Popular Question 7 months ago, created a question with more than 1,000 views. For pytabix - quickly retrieve rows from a table of positions or regions
Popular Question 7 months ago, created a question with more than 1,000 views. For Quick statistics from the command line
Scholar 9 months ago, created an answer that has been accepted. For A: PWM Scan For Toxoplasma gondii
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Path
Popular Question 12 months ago, created a question with more than 1,000 views. For Quick statistics from the command line
Appreciated 13 months ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Popular Question 13 months ago, created a question with more than 1,000 views. For Quick statistics from the command line
Prophet 14 months ago, created a post with more than 20 followers. For FASTA and FASTQ tools
Popular Question 14 months ago, created a question with more than 1,000 views. For ggrepel: repel overlapping text labels in ggplot2
Popular Question 20 months ago, created a question with more than 1,000 views. For FASTA and FASTQ tools
Autobiographer 21 months ago, has more than 80 characters in the information field of the user's profile.
Appreciated 21 months ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Guru 23 months ago, received more than 100 upvotes.
Scholar 23 months ago, created an answer that has been accepted. For A: PWM Scan For Toxoplasma gondii
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: span of GFF file
Scholar 23 months ago, created an answer that has been accepted. For A: PWM Scan For Toxoplasma gondii
Scholar 2.0 years ago, created an answer that has been accepted. For A: PWM Scan For Toxoplasma gondii

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