Showing : genomicfeatures • reset
9
votes
21
replies
11k
views
annotate GRanges with upstream or downstream nearest gene
GRange genomicranges genomicfeatures
updated 8.3 years ago by ★ 1.3k • written 8.3 years ago by ▴ 190
0
votes
2
replies
7.9k
views
Error with "library("GenomicFeatures")" - "there is no package called ‘XML’"
genomicfeatures xml loadnamespace
9.0 years ago greg.mulhearn • 0
1
vote
7
replies
6.2k
views
Existence of a makeTxDbFromGFF function in GenomicFeatures package?
genomicfeatures
9.0 years ago pterry • 0
8
votes
3
replies
6.2k
views
Renaming the seqlevels in a transcript database from GenomicFeatures
GenomicFeatures GenomicFeatures
updated 9.8 years ago by ▴ 390 • written 9.8 years ago by ▴ 320
6
votes
14
replies
5.9k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 9.3 years ago by 50k • written 9.3 years ago by • 0
8
votes
20
replies
5.6k
views
Issue when import genomic features from the file :Error in parseURI("") : cannot parse URI (issue resolved)
genomicfeatures xml libxml2
7.2 years ago • updated 7.1 years ago JunLVI ▴ 40
8
votes
12
replies
5.5k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 21 months ago by • 0 • written 9.1 years ago by ▴ 20
0
votes
4
replies
5.1k
views
Problem installing GenomicFeatures
GenomicFeatures GenomicFeatures
12.1 years ago Georg Otto ▴ 120
2
votes
7
replies
4.9k
views
Extend GRanges start/end
Genetics GenomicFeatures Genetics GenomicFeatures
updated 11.5 years ago by ★ 11k • written 11.5 years ago by ▴ 490
0
votes
8
replies
4.8k
views
error making txdb object from gtf file
genomicfeatures
updated 8.3 years ago by ★ 2.0k • written 8.3 years ago by ▴ 20
2
votes
2
replies
4.7k
views
Could not find function "makeTranscriptDbFromGFF"
GenomicFeatures makeTranscriptDbFromGFF gff annotation
updated 6.6 years ago by ★ 11k • written 6.6 years ago by ▴ 20
6
votes
5
replies
4.6k
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 24 months ago by 16k • written 5.2 years ago by • 0
0
votes
1
reply
4.4k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 90
2
votes
4
replies
4.3k
views
Gene Size using GenomicFeatures
genomicfeatures gene size gene length
updated 6.6 years ago by 16k • written 6.6 years ago by • 0
3
votes
10
replies
4.3k
views
Getting a list of all tRNA encoding genes for an organism?
trna ncrna genomicfeatures featuredb biomart
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 180
2
votes
16
replies
4.1k
views
TxDb annotations for human chrM
GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene annotation
9.3 years ago • updated 9.2 years ago Robert Castelo ★ 3.3k
0
votes
5
replies
3.9k
views
Failed to obtain \'hguid\' cookie for UCSC browser session
GenomicFeatures GenomicFeatures
updated 10.8 years ago by ★ 8.2k • written 10.8 years ago by ★ 13k
4
votes
3
replies
3.8k
views
subsetting GRanges object based on gene IDs
genomicranges genomicfeatures granges subsetting
6.6 years ago Assa Yeroslaviz ★ 1.5k
5
votes
6
replies
3.7k
views
error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 5.2 years ago by 16k • written 5.3 years ago by • 0
0
votes
9
replies
3.7k
views
genomicfeatures rsqlite database or disk is full
genomicfeatures
updated 9.1 years ago by ★ 7.2k • written 9.1 years ago by ▴ 90
0
votes
3
replies
3.6k
views
makeTxDbFromGFF Error: subscript contains NAs
genomicfeatures granges maketxdbfromgff
updated 6.7 years ago by 16k • written 6.8 years ago by • 0
0
votes
4
replies
3.5k
views
Get all 3'utr and 5'utr region from GenomicFeatures
GenomicFeatures GenomicFeatures
updated 12.9 years ago by 65k • written 12.9 years ago by ▴ 970
3
votes
5
replies
3.5k
views
Error with ChIPpeakAnno Ensembl annotation
ChIPpeakAnno genomicfeatures
updated 7.4 years ago by ★ 4.3k • written 7.4 years ago by ▴ 360
3
votes
10
replies
3.5k
views
CDS phase information missing from GenomicFeatures
GenomicFeatures phase gene models GFF
updated 6.5 years ago by 16k • written 6.6 years ago by ▴ 10
0
votes
18
replies
3.5k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
2.2 years ago rbenel ▴ 40
0
votes
5
replies
3.5k
views
Fast way to find which gene a snp located.
SNP GenomicFeatures SNP GenomicFeatures
updated 13.0 years ago by ▴ 10 • written 13.0 years ago by ▴ 970
8
votes
24
replies
3.5k
views
GenomicFeatures: Select exons by transcript. Any faster option than exonsBy?
GenomicFeatures
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 90
0
votes
3
replies
3.4k
views
‘GenomicFeatures’ is not available (for R version 3.2.0)
genomicfeatures
updated 8.9 years ago by ▴ 10 • written 8.9 years ago by • 0
1
vote
10
replies
3.4k
views
Issue creating a genomic state object in derfinder from an Ensembl GTF file
derfinder genomicfeatures
7.2 years ago Leonardo Collado Torres ★ 1.0k
0
votes
6
replies
3.2k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster quasR genomicfeatures genomicranges alignment
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 70
3
votes
2
replies
3.2k
views
Cannot install GenomicFeatures package (related to RSQLite version)
biocinstaller genomicfeatures rsqlite
updated 9.4 years ago by ★ 8.2k • written 9.4 years ago by • 0
5
votes
2
replies
3.2k
views
Saving/loading TxDb objects
genomicfeatures
updated 8.9 years ago by 25k • written 8.9 years ago by 65k
1
vote
14
replies
3.2k
views
DEXSeq - dexseq_count.py issue
dexseq dexseq_count genomicfeatures
updated 6.0 years ago by • 0 • written 6.1 years ago by • 0
4
votes
5
replies
3.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 3 months ago by ▴ 10 • written 8.4 years ago by ▴ 10
4
votes
3
replies
3.1k
views
TxDb error: external pointer is not valid
software error GenomicFeatures
4.6 years ago O. William McClung • 0
3
votes
13
replies
3.1k
views
Getting errors with makeTxDbFromBiomart
genomicfeatures biomart maketxdbfrombiomart
updated 7.3 years ago by ▴ 800 • written 7.3 years ago by ▴ 10
0
votes
2
replies
3.1k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 3.5 years ago by 41k • written 3.5 years ago by • 0
0
votes
4
replies
3.0k
views
How can I extract promoter regions from a list NCBI genbank acc?
GenomicFeatures GenomicFeatures
updated 11.5 years ago by ★ 7.2k • written 11.5 years ago by ▴ 200
9
votes
3
replies
3.0k
views
Importing Gene Symbols with makeTxDbFromGFF
GenomicFeatures GFF3
updated 7.1 years ago by ★ 6.8k • written 7.1 years ago by ★ 1.5k
1
vote
8
replies
3.0k
views
GenomicFeatures package ERROR
software error genomicfeatures
updated 6.9 years ago by ★ 11k • written 8.4 years ago by • 0
3
votes
7
replies
2.9k
views
Failed to set session genome to ...
genomicfeatures makeTxDbFromUCSC
updated 8.5 years ago by ★ 11k • written 9.0 years ago by ▴ 100
0
votes
10
replies
2.8k
views
GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer RNAseqData GenomicFeatures Cancer RNAseqData GenomicFeatures
updated 9.8 years ago by ▴ 320 • written 9.8 years ago by ★ 6.8k
0
votes
5
replies
2.7k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.1 years ago sieminsk • 0
0
votes
13
replies
2.7k
views
multiple hits with countOverlaps function
Sequencing GenomicFeatures Sequencing GenomicFeatures
13.0 years ago Wei Shi ★ 3.6k
3
votes
5
replies
2.7k
views
makeTxDbFromGFF Error: subscript contains NAs or out-of-bounds indices - after package update
genomicfeatures
updated 7.9 years ago by 16k • written 7.9 years ago by • 0
4
votes
7
replies
2.7k
views
How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembly?
makeTxDbFromBiomart genomicfeatures txdb biomart
updated 8.5 years ago by 65k • written 8.5 years ago by ▴ 50
8
votes
16
replies
2.7k
views
Setting package name in makeTxDbPackage
genomicfeatures txdb
updated 8.9 years ago by ★ 7.2k • written 9.0 years ago by ▴ 760
1
vote
2
replies
2.6k
views
GenomicFeatures::getPromoterSeq error when selecting all promoters sequences (in mice)
GenomicFeatures getPromoterSeq
updated 9.4 years ago by 65k • written 9.4 years ago by ▴ 120
6
votes
7
replies
2.6k
views
makeTxDbFromUCSC fails to download refLink table
genomicfeatures maketxdbfromucsc refseq
updated 7.8 years ago by 16k • written 7.8 years ago by ▴ 10
1
vote
2
replies
2.5k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 7.8 years ago by 16k • written 7.8 years ago by ★ 3.9k
50 results • Page 1 of 1
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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