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1.5k
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Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
2.4 years ago Bogdan ▴ 670
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0
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1.5k
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conversion a VCF file into a MAF file
VCFArray maftools
2.6 years ago Bogdan ▴ 670
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2
replies
2.1k
views
about baseMean in DEseq2
DESeq2
written 4.6 years ago by ▴ 670
0
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1
reply
1.1k
views
BioC packages in cancer genomics
genomics cancer
updated 3.0 years ago by ★ 4.0k • written 3.0 years ago by ▴ 670
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1
reply
1.2k
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GRanges list convert into igraph format
GRanges igraph
updated 3.1 years ago by ▴ 760 • written 3.1 years ago by ▴ 670
0
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0
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841
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normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
3.2 years ago Bogdan ▴ 670
0
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0
replies
866
views
RUVg for SNAP-ChIP ?
RUVSeq
3.2 years ago Bogdan ▴ 670
1
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12
replies
4.0k
views
normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2 edgeR limma
updated 3.2 years ago by 43k • written 3.3 years ago by ▴ 670
2
votes
4
replies
1.8k
views
DiffBind and peak counts as input
DESeq2 edgeR DiffBind
updated 3.2 years ago by ★ 5.3k • written 3.4 years ago by ▴ 670
1
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7
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1.8k
views
statistics : edger or DESeq2 to asses the differential binding using the average scores
DESeq2 edgeR
updated 3.2 years ago by • 0 • written 3.4 years ago by ▴ 670
3
votes
9
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2.4k
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scDblFinder and xgboost
scDblFinder xgboost
written 3.8 years ago by ▴ 670
0
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3
replies
2.7k
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ShortRead Installation in R 4.2.0 and zlib library
R-4 ShortRead
3.4 years ago Bogdan ▴ 670
1
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1
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3.7k
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installation of BioC packages on Mac M1 Monterrey OS
limma Bioconductor edgeR
3.4 years ago Bogdan ▴ 670
0
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1
reply
2.6k
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bigwig to counts
DESeq2 edgeR bigwig limma
3.4 years ago • updated 3.1 years ago Bogdan ▴ 670
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2
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3.0k
views
converting bedgraph into bigwig
bedgraph wiggleplotr bigwig wig
updated 3.5 years ago by • 0 • written 3.5 years ago by ▴ 670
0
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6
replies
2.9k
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 2.9 years ago by • 0 • written 3.8 years ago by ▴ 670
0
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6
replies
2.3k
views
scDblFinder and amulet
scDblFinder
updated 3.8 years ago by • 0 • written 3.8 years ago by ▴ 670
3
votes
5
replies
3.9k
views
reading hdf5 files without hdf5r
hdf5r
updated 3.8 years ago by 16k • written 3.8 years ago by ▴ 670
0
votes
1
reply
924
views
download
BSgenome.Hsapiens.UCSC.hg38 BSgenome.Hsapiens.UCSC.hg38.masked
3.8 years ago Bogdan ▴ 670
0
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1
reply
1.4k
views
scATAC-seq median fragments per cell
SnapATAC Signac ArchR scATAC-seq
3.9 years ago Bogdan ▴ 670
1
vote
1
reply
2.1k
views
installing the packages such as BSgenome.Hsapiens.UCSC.hg19
BSgenome.Hsapiens.UCSC.hg19
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 670
0
votes
1
reply
1.4k
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peak annotation
ChIPpeakAnno Annotation
updated 3.9 years ago by ▴ 70 • written 4.0 years ago by ▴ 670
1
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2
replies
2.4k
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Gviz and datatracks
Gviz
updated 4.0 years ago by • 0 • written 4.1 years ago by ▴ 670
0
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1
reply
1.6k
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meta-gene profiles
ChIP-seq
updated 4.0 years ago by ▴ 60 • written 4.0 years ago by ▴ 670
0
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1
reply
1.6k
views
saving png images and X11
ChipQC
updated 4.0 years ago by ★ 5.0k • written 4.0 years ago by ▴ 670
0
votes
2
replies
1.7k
views
ChIP-seq or CUT&RUN enrichment
ChIPQC ChIPpeakAnno
4.1 years ago • updated 4.0 years ago Bogdan ▴ 670
0
votes
0
replies
1.4k
views
about monocle3
monocle3
4.3 years ago Bogdan ▴ 670
0
votes
2
replies
2.5k
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AnnotationDbi
AnnotationDbi
4.3 years ago Bogdan ▴ 670
0
votes
8
replies
3.8k
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TCL/TK in R
TCL/TK
4.4 years ago • updated 4.3 years ago Bogdan ▴ 670
0
votes
0
replies
901
views
packages for integrative genomics
genomics integrative GenomicSequence
4.5 years ago Bogdan ▴ 670
1
vote
2
replies
1.2k
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gene ontologies for a set of genes
gene ontology
4.6 years ago Bogdan ▴ 670
0
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6
replies
7.7k
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extracting the KEGG pathway for a set of genes
Pathways KEGG
4.6 years ago Bogdan ▴ 670
0
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3
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1.2k
views
identifying trends in RNA-seq data
RNASeq trend
updated 4.6 years ago by ★ 5.0k • written 4.6 years ago by ▴ 670
5
votes
2
replies
26k
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about MapIds function
mapIds
4.6 years ago Bogdan ▴ 670
0
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0
replies
885
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visualization of circRNA
circRNA circRNAprofiler
4.6 years ago Bogdan ▴ 670
0
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0
replies
1.2k
views
display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
5.0 years ago Bogdan ▴ 670
6
votes
5
replies
3.3k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
5.2 years ago Bogdan ▴ 670
0
votes
1
reply
999
views
a BioC/R package that display the genome sequence/ mRNA exons/protein domains
AnnotationHubData
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 670
5
votes
10
replies
2.8k
views
analysis of FACS data using BioC
facs prada flowstats
5.4 years ago Bogdan ▴ 670
0
votes
0
replies
1.2k
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq time series
5.6 years ago Bogdan ▴ 670
0
votes
3
replies
1.8k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 670
1
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1
reply
961
views
a package with randomization/permutation tests for genomic analyses
normalization
6.0 years ago Bogdan ▴ 670
0
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0
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844
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permutation and randomization tests
permutation randomization
6.0 years ago Bogdan ▴ 670
3
votes
11
replies
3.3k
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 6.1 years ago by ★ 29k • written 6.1 years ago by ▴ 670
0
votes
5
replies
2.2k
views
analysis of multiple time points * 2 replicates of scRNA-seq
scRNAseq
updated 6.1 years ago by ★ 29k • written 6.1 years ago by ▴ 670
4
votes
2
replies
1.2k
views
scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
scRNA-seq
updated 6.1 years ago by ★ 29k • written 6.1 years ago by ▴ 670
0
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6
replies
2.5k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 6.5 years ago by ▴ 280 • written 6.6 years ago by ▴ 670
6
votes
4
replies
4.3k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 670
4
votes
4
replies
3.9k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 670
4
votes
4
replies
1.5k
views
normalization of RNA-seq data after over-expressing the transcription factors
limma deseq2 voom edgeR
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 670
170 results • Page 1 of 4
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