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0
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430
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Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
6 months ago Bogdan ▴ 670
0
votes
0
replies
543
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conversion a VCF file into a MAF file
VCFArray maftools
8 months ago Bogdan ▴ 670
0
votes
2
replies
1.3k
views
about baseMean in DEseq2
DESeq2
written 2.7 years ago by ▴ 670
0
votes
1
reply
525
views
BioC packages in cancer genomics
genomics cancer
updated 13 months ago by ★ 3.9k • written 13 months ago by ▴ 670
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1
reply
605
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GRanges list convert into igraph format
GRanges igraph
updated 15 months ago by ▴ 730 • written 15 months ago by ▴ 670
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0
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444
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normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
16 months ago Bogdan ▴ 670
0
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0
replies
452
views
RUVg for SNAP-ChIP ?
RUVSeq
16 months ago Bogdan ▴ 670
1
vote
12
replies
2.3k
views
normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2 edgeR limma
updated 16 months ago by 41k • written 17 months ago by ▴ 670
2
votes
4
replies
1.0k
views
DiffBind and peak counts as input
DESeq2 edgeR DiffBind
updated 16 months ago by ★ 5.1k • written 18 months ago by ▴ 670
1
vote
7
replies
984
views
statistics : edger or DESeq2 to asses the differential binding using the average scores
DESeq2 edgeR
updated 16 months ago by • 0 • written 18 months ago by ▴ 670
3
votes
9
replies
1.5k
views
scDblFinder and xgboost
scDblFinder xgboost
written 23 months ago by ▴ 670
0
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3
replies
1.3k
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ShortRead Installation in R 4.2.0 and zlib library
R-4 ShortRead
18 months ago Bogdan ▴ 670
1
vote
1
reply
2.3k
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installation of BioC packages on Mac M1 Monterrey OS
limma Bioconductor edgeR
18 months ago Bogdan ▴ 670
0
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1
reply
1.4k
views
bigwig to counts
DESeq2 edgeR bigwig limma
18 months ago • updated 15 months ago Bogdan ▴ 670
0
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2
replies
1.6k
views
converting bedgraph into bigwig
bedgraph wiggleplotr bigwig wig
updated 19 months ago by • 0 • written 20 months ago by ▴ 670
0
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6
replies
1.7k
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performing the differential binding in ChIP-seq
ChIP-seq
updated 12 months ago by • 0 • written 23 months ago by ▴ 670
0
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6
replies
1.2k
views
scDblFinder and amulet
scDblFinder
updated 23 months ago by • 0 • written 23 months ago by ▴ 670
3
votes
5
replies
2.0k
views
reading hdf5 files without hdf5r
hdf5r
updated 23 months ago by 16k • written 24 months ago by ▴ 670
0
votes
1
reply
506
views
download
BSgenome.Hsapiens.UCSC.hg38 BSgenome.Hsapiens.UCSC.hg38.masked
24 months ago Bogdan ▴ 670
0
votes
1
reply
802
views
scATAC-seq median fragments per cell
SnapATAC Signac ArchR scATAC-seq
2.1 years ago Bogdan ▴ 670
1
vote
1
reply
1.1k
views
installing the packages such as BSgenome.Hsapiens.UCSC.hg19
BSgenome.Hsapiens.UCSC.hg19
updated 2.1 years ago by 16k • written 2.1 years ago by ▴ 670
0
votes
1
reply
780
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peak annotation
ChIPpeakAnno Annotation
updated 2.0 years ago by ▴ 70 • written 2.1 years ago by ▴ 670
1
vote
2
replies
1.4k
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Gviz and datatracks
Gviz
updated 2.1 years ago by • 0 • written 2.3 years ago by ▴ 670
0
votes
1
reply
712
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meta-gene profiles
ChIP-seq
updated 2.1 years ago by ▴ 60 • written 2.1 years ago by ▴ 670
0
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1
reply
882
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saving png images and X11
ChipQC
updated 2.1 years ago by ★ 4.0k • written 2.1 years ago by ▴ 670
0
votes
2
replies
874
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ChIP-seq or CUT&RUN enrichment
ChIPQC ChIPpeakAnno
2.2 years ago Bogdan ▴ 670
0
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0
replies
808
views
about monocle3
monocle3
2.5 years ago Bogdan ▴ 670
0
votes
2
replies
1.4k
views
AnnotationDbi
AnnotationDbi
2.5 years ago Bogdan ▴ 670
0
votes
8
replies
2.3k
views
TCL/TK in R
TCL/TK
2.5 years ago Bogdan ▴ 670
0
votes
0
replies
550
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packages for integrative genomics
genomics integrative GenomicSequence
2.6 years ago Bogdan ▴ 670
1
vote
2
replies
718
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gene ontologies for a set of genes
gene ontology
2.7 years ago Bogdan ▴ 670
0
votes
6
replies
3.6k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
2.7 years ago Bogdan ▴ 670
0
votes
3
replies
689
views
identifying trends in RNA-seq data
RNASeq trend
updated 2.7 years ago by ★ 4.0k • written 2.7 years ago by ▴ 670
5
votes
2
replies
15k
views
about MapIds function
mapIds
2.8 years ago Bogdan ▴ 670
0
votes
0
replies
495
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visualization of circRNA
circRNA circRNAprofiler
2.8 years ago Bogdan ▴ 670
0
votes
0
replies
726
views
display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
3.2 years ago Bogdan ▴ 670
6
votes
5
replies
1.5k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.4 years ago Bogdan ▴ 670
0
votes
1
reply
621
views
a BioC/R package that display the genome sequence/ mRNA exons/protein domains
AnnotationHubData
updated 3.4 years ago by ★ 3.9k • written 3.4 years ago by ▴ 670
5
votes
10
replies
1.6k
views
analysis of FACS data using BioC
facs prada flowstats
3.6 years ago Bogdan ▴ 670
0
votes
0
replies
652
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq time series
3.8 years ago Bogdan ▴ 670
0
votes
3
replies
1.1k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 670
1
vote
1
reply
673
views
a package with randomization/permutation tests for genomic analyses
normalization
4.1 years ago Bogdan ▴ 670
0
votes
0
replies
481
views
permutation and randomization tests
permutation randomization
4.2 years ago Bogdan ▴ 670
3
votes
11
replies
1.8k
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 670
0
votes
5
replies
1.5k
views
analysis of multiple time points * 2 replicates of scRNA-seq
scRNAseq
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 670
4
votes
2
replies
726
views
scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
scRNA-seq
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 670
0
votes
6
replies
1.7k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by ▴ 670
6
votes
4
replies
2.6k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 4.7 years ago by 25k • written 4.7 years ago by ▴ 670
4
votes
4
replies
2.8k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 4.7 years ago by ★ 28k • written 4.8 years ago by ▴ 670
4
votes
4
replies
962
views
normalization of RNA-seq data after over-expressing the transcription factors
limma deseq2 voom edgeR
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 670
170 results • Page 1 of 4
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