Showing : gff3 • reset
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DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq python gtf gff3 annotation
4.6 years ago Raito92 ▴ 60
2
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2
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2.3k
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Filtering GFF3 file
annotation gff3 gff genome
updated 5.3 years ago by ★ 11k • written 5.3 years ago by ▴ 10
0
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0
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1.1k
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I need to measure distance of PAR-CLIP data to RNA regions
parclip bedtools bed files gff3
6.9 years ago linuxborg2 • 0
2
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2
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5.0k
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How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
7.1 years ago Piotr Gawronski • 0
9
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3
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3.5k
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Importing Gene Symbols with makeTxDbFromGFF
GenomicFeatures GFF3
updated 7.8 years ago by ★ 6.8k • written 7.8 years ago by ★ 1.5k
2
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0
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3.7k
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News: Gencode GFF3 and FASTA files now available via AnnotationHub
AnnotationHub Gencode GFF3 FASTA News
9.3 years ago Sonali Arora ▴ 390
6 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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