Bioconductor Samtools

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samtools bcftools

updated 2.4 years ago by Kevin Blighe 3.9k • written 2.4 years ago by mike_flower • 0

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samtools tabix VariantAnnotation VCFArray

updated 2.7 years ago by Vincent J. Carey, Jr. 6.7k • written 2.8 years ago by naive • 0

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SAM samtools pairwisealignment alignment blastn

5.3 years ago ktehmsen • 0

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rsamtools samtools bam bowtie2

5.8 years ago igor ▴ 40

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rsamtools package installation samtools

updated 6.0 years ago by James W. MacDonald 64k • written 6.0 years ago by rbronste ▴ 60

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samtools rsamtools

updated 6.3 years ago by Martin Morgan 25k • written 6.3 years ago by rbronste ▴ 60

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diffbind samtools

updated 6.6 years ago by Gord Brown ▴ 650 • written 6.6 years ago by sergio.espeso-gil • 0

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samtools

7.2 years ago josh_banta • 0

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gviz GenomeGraphs BAM rsamtools samtools

updated 7.3 years ago by Martin Morgan 25k • written 7.3 years ago by Mehmet Ilyas Cosacak • 0

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bam rsamtools samtools genomicalignments

updated 7.6 years ago by Martin Morgan 25k • written 7.6 years ago by Vang Le ▴ 80

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python samtools

updated 8.1 years ago by Hervé Pagès 16k • written 8.2 years ago by malikbashirkhan2 • 0

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samtools bioinformatics

8.5 years ago engr.yahya602 • 0

12 results • Page 1 of 1

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Comment: DuplicateCorrelation() block by duplicate sample or by cell line ? by Gordon Smyth 49k

They are not technical replicates. With the `Exposure+CellLine` model, your experiment has only one level of variability so there is no pos…

Comment: DuplicateCorrelation() block by duplicate sample or by cell line ? by Gimena • 0

Hi James, Yes, these are complete cases. every line has all the treatment groups and technical replicates.

Comment: DuplicateCorrelation() block by duplicate sample or by cell line ? by Gimena • 0

I am sorry for the confusion. It goes like this: 3 drug exposures (vehicle, low and high dose) x 2 replicates per condition: technical re…

Comment: How does Deseq2 deal with the row with zero when calculating size factors by jiakang • 0

Thanks for your quick reply. I understand and have noticed the code you mentioned above. > the size factors results of sfType = "poscount…

Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

Yes. I considered genome wide p value as cutoff.

Votes

Attempting to import SBML file using R

Answer: RNASeq time course analysis, missing time points for control

Answer: biomaRt not working - lazy table error

Answer: Confused about the CPM and TMM normalization in edgeR

Answer: Differential gene expression analysis

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