User: Kamil

gravatar for Kamil
Kamil1.8k
Reputation:
1,780
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Trusted
Location:
Boston
Website:
http://slowkow.com/
Twitter:
slowkow
Scholar ID:
Google Scholar Page
Last seen:
5 days, 7 hours ago
Joined:
8 years, 2 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 13 months ago by Kamil1.8k
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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 13 months ago by Kamil1.8k
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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 21 months ago by Kamil1.8k
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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 21 months ago by Kamil1.8k
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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 23 months ago by Kamil1.8k
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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][1] for more information. [1]: https://pachterlab.github.io/kallisto/manual ...
written 2.0 years ago by Kamil1.8k • updated 4 weeks ago by RamRS18k
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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 2.0 years ago by Kamil1.8k
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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 2.5 years ago by Kamil1.8k
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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][1]: limma, DESeq, edgeR, etc. [1]: https://www.bioconductor.o ...
written 2.7 years ago by Kamil1.8k • updated 4 weeks ago by RamRS18k
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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 2.7 years ago by Kamil1.8k

Latest awards to Kamil

Great Question 4 months ago, created a question with more than 5,000 views. For FASTA and FASTQ tools
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Calculating TPM from featureCounts output
Appreciated 8 months ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Appreciated 10 months ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Calculating TPM from featureCounts output
Appreciated 11 months ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Teacher 12 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 13 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
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Tutorials for Library Normalization in DESeq2 and EdgeR
Librarian 13 months ago, created a post with more than 10 bookmarks. For FASTA and FASTQ tools
Appreciated 13 months ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Teacher 17 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 18 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 18 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 19 months ago, created a question with more than 1,000 views. For Quick statistics from the command line
Scholar 20 months ago, created an answer that has been accepted. For A: PWM Scan For Toxoplasma gondii
Teacher 21 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 23 months ago, created a question with more than 1,000 views. For Quick statistics from the command line
Appreciated 24 months ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Quick statistics from the command line
Popular Question 2.1 years ago, created a question with more than 1,000 views. For ggrepel: repel overlapping text labels in ggplot2
Prophet 2.1 years ago, created a post with more than 20 followers. For FASTA and FASTQ tools
Popular Question 2.6 years ago, created a question with more than 1,000 views. For FASTA and FASTQ tools
Autobiographer 2.7 years ago, has more than 80 characters in the information field of the user's profile.
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites

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