Showing : GenomicFeatures • reset
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how to match salmon output to txname
GenomicFeatures tximport salmon
written 25 days ago by • 0
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5
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242
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Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 8 weeks ago by 62k • written 8 weeks ago by • 0
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100
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Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
3 months ago nattzy94 ▴ 20
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2
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285
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How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 4 months ago by 39k • written 4 months ago by ▴ 10
0
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4
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761
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error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 8 months ago by 16k • written 8 months ago by • 0
5
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9
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751
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Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 6 months ago by 39k • written 10 months ago by • 0
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18
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1.7k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
12 months ago • updated 11 months ago rbenel ▴ 20
3
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3
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878
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GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 9 months ago by 62k • written 13 months ago by ▴ 30
1
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2
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588
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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
14 months ago Madza Farias-Virgens • 0
2
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3
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1.0k
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How to get longest isoform
GenomicFeatures Biostrings
updated 14 months ago by 16k • written 14 months ago by • 0
1
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2
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457
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NAs in my txdb tx_name
GenomicFeatures Biostrings
14 months ago Madza Farias-Virgens • 0
2
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2
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418
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Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 14 months ago by 16k • written 15 months ago by • 0
5
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2
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591
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
16 months ago Pratik Mehta ▴ 10
0
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1
reply
481
views
install GenomicFeatures fail
GenomicFeatures install
updated 17 months ago by 62k • written 17 months ago by ▴ 80
1
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4
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638
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
18 months ago A.J. ▴ 20
1
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3
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509
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Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
18 months ago A.J. ▴ 20
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0
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344
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
18 months ago Matthias Munz ▴ 10
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0
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410
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annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
21 months ago António Miguel de Jesus Domingues ▴ 490
0
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5
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1.4k
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Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
22 months ago sieminsk • 0
2
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2
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899
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makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
23 months ago erhoppe • 0
0
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6
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659
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Splitting TxDb by Strand
GenomicFeatures TxDb
24 months ago rproendo ▴ 20
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3
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508
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Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 15 months ago by • 0 • written 2.2 years ago by ▴ 120
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2
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1.7k
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Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 2.3 years ago by 39k • written 2.3 years ago by • 0
0
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1
reply
397
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pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 24 months ago by ▴ 80 • written 2.3 years ago by ▴ 10
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1
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2.3k
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Add gene symbol when making TxDb
txdb genomicfeatures
updated 2.5 years ago by 62k • written 2.5 years ago by ▴ 90
3
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7
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904
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GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 2.5 years ago by 62k • written 2.5 years ago by ▴ 20
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1
reply
641
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 2.5 years ago by 3.4k • written 2.5 years ago by • 0
3
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6
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870
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TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 2.6 years ago by 25k • written 2.6 years ago by ▴ 120
0
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1
reply
548
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 2.7 years ago by 62k • written 2.7 years ago by ▴ 100
0
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2
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471
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How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 2.7 years ago by 11k • written 2.7 years ago by ▴ 10
0
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0
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490
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A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
2.8 years ago Guandong Shang ▴ 40
0
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2
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346
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Error with makeTxDbFromBiomart
GenomicFeatures
updated 2.8 years ago by 62k • written 2.8 years ago by ▴ 40
2
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3
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975
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 2.8 years ago by 62k • written 2.8 years ago by ▴ 80
3
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4
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614
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how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 40
1
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2
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480
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 2.9 years ago by 13k • written 2.9 years ago by ▴ 40
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0
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472
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 3.0 years ago by 3.4k • written 3.0 years ago by • 0
0
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2
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563
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biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 3.0 years ago by 62k • written 3.0 years ago by • 0
8
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12
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4.0k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 6 months ago by • 0 • written 7.9 years ago by ▴ 20
2
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3
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518
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GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 3.0 years ago by 62k • written 3.0 years ago by ▴ 20
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3
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532
views
Resize exons in transcript to total width
genomicranges genomicfeatures
updated 3.1 years ago by 11k • written 3.1 years ago by ▴ 90
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8
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801
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exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 3.2 years ago by 16k • written 3.2 years ago by ▴ 90
2
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0
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426
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SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
3.2 years ago rmash ▴ 20
4
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3
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2.1k
views
TxDb error: external pointer is not valid
software error GenomicFeatures
3.4 years ago • updated 3.3 years ago O. William McClung • 0
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2
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668
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Error while creating txDb from gtf file
genomicfeatures
3.4 years ago bioinagesh • 0
5
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5
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960
views
threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 23 months ago by ★ 1.5k • written 3.4 years ago by ▴ 10
0
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1
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696
views
create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 3.8 years ago by 16k • written 3.8 years ago by ▴ 10
0
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0
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932
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error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
3.8 years ago xvazquezc • 0
0
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0
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461
views
Features function from genomicFeatures package worked in 2014 but currently doesn't work (upload of a deleted post)
genomicfeatures
updated 3.9 years ago by 25k • written 3.9 years ago by • 0
4
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5
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2.6k
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 9 months ago by 16k • written 4.0 years ago by • 0
5
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6
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1.3k
views
error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 4.0 years ago by 16k • written 4.0 years ago by • 0
50 results • Page 1 of 1
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Comment: mas5calls function doesn't work; mirna40cdf problem by James W. MacDonald 62k
Yes. Follow the recommendation in the link that was provided to you by Lori Shepherd.
Comment: mas5calls function doesn't work; mirna40cdf problem by Berna • 0
Thank you for the information. I did not know that. Would you have a tip how I could proceed differently?
Comment: Correct use of Likelihood Ratio Test and LFC Shrinkage by ayabalbaa1990 • 0
Hi Michael, So I use this res_LRT <- results(dds_lrt) r2=lfcShrink(dds_lrt, coef=7, res=res_LRT) tu run lfcshrink with LRT, is that oko?…
Comment: Combat and dds Object by shaimaa • 0
I used the combat-seq but the deseq complain as its not integer what should i do
Answer: Different summary() and results() values in DeSeq2 by Basti ▴ 540
summary() tells you the number of genes with low counts, see independant filtering of results in the DESeq2 vignette : https://www.biocondu…
Votes
Answer: mas5calls function doesn't work; mirna40cdf problem
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings
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Popular Question to Guido Hooiveld ★ 3.5k
Scholar to James W. MacDonald 62k
Commentator to Michael Love 39k
Popular Question to twtoal ▴ 10
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