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6
votes
4
replies
840
views
Problematic experimental design RNA-Seq
RNA-Seq
updated 11 months ago by 82k • written 12 months ago by ★ 2.6k
1
vote
2
replies
553
views
Cleaning File system in bioinformatics
Filesystem
22 months ago by grant.hovhannisyan ★ 2.6k
3
votes
2
replies
986
views
_1 in gene_ids of human T2T assemby gtf file
gtf T2T
updated 22 months ago by ★ 3.7k • written 22 months ago by ★ 2.6k
5
votes
7
replies
1.2k
views
Public servers for bioinformatics
computational resources
22 months ago by grant.hovhannisyan ★ 2.6k
2
votes
4
replies
4.4k
views
relevel the clusterProfiler object
clusterProfiler
2.7 years ago by grant.hovhannisyan ★ 2.6k
2
votes
5
replies
2.7k
views
download all metadata from SRA
SRA
2.7 years ago by grant.hovhannisyan ★ 2.6k
3
votes
3
replies
1.0k
views
probability of observing overlap between sets of genes
R
updated 3.2 years ago by 20 • written 4.7 years ago by ★ 2.6k
9
votes
6
replies
11k
views
LEADING and TRAILING in TRIMMOMATIC
RNA-Seq trimmomatic
updated 4.1 years ago by ▴ 10 • written 5.9 years ago by ★ 2.6k
3
votes
4
replies
2.3k
views
Library type warning in Salmon
Salmon RNAseq library-type
updated 4.2 years ago by 20 • written 6.1 years ago by ★ 2.6k
1
vote
3
replies
1.2k
views
RNAfold discriminant error
RNAfold
4.2 years ago by grant.hovhannisyan ★ 2.6k
2
votes
5
replies
2.1k
views
wgcna network interpretation
wgcna
updated 4.2 years ago by 19k • written 4.2 years ago by ★ 2.6k
5
votes
3
replies
6.0k
views
Hub selection in WGCNA
wgcna hubs
updated 4.2 years ago by 87k • written 4.2 years ago by ★ 2.6k
3
votes
4
replies
1.2k
views
Retrieve "Abstract" of SRP accession from SRA
sra
updated 4.3 years ago by 142k • written 4.3 years ago by ★ 2.6k
6
votes
8
replies
1.4k
views
P-value of expected/observed proportion
stats
4.4 years ago by grant.hovhannisyan ★ 2.6k
0
votes
2
replies
1.3k
views
collapseReplicates changes the order of the original dataframe in DESeq2
DESeq2 collapseReplicates
4.8 years ago by grant.hovhannisyan ★ 2.6k
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq RNA-Seq batch-effect DESeq2
updated 16 days ago by 43k • written 5.1 years ago by ★ 2.6k
5
votes
4
replies
3.9k
views
ClusterProfiler fails to find GO terms
RNA-Seq GO clusterProfiler
updated 2.7 years ago by • 0 • written 5.1 years ago by ★ 2.6k
3
votes
2
replies
2.7k
views
unmapped reads with pysam
pysam
5.3 years ago by grant.hovhannisyan ★ 2.6k
0
votes
1
reply
2.2k
views
same transcript id with STAR quant mode
RNA-Seq STAR gtf
updated 5.3 years ago by ★ 1.3k • written 6.4 years ago by ★ 2.6k
1
vote
7
replies
3.1k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT TF-footprinting ATAC-seq
updated 11 months ago by 43k • written 5.4 years ago by ★ 2.6k
6
votes
6
replies
1.2k
views
Restriction in read name length
read name
updated 5.5 years ago by 161k • written 5.5 years ago by ★ 2.6k
4
votes
3
replies
992
views
Specific DE comparisons with complex design matrix
DESeq2
updated 5.5 years ago by 14k • written 5.5 years ago by ★ 2.6k
12
votes
23
replies
8.4k
views
6 follow
motif search with ATAC-seq
motif-search ATAC-seq
updated 11 months ago by 43k • written 5.6 years ago by ★ 2.6k
1
vote
5
replies
1.9k
views
Wrong coordinates of peaks in DiffBind
DiffBind ATAC-seq
updated 11 months ago by 43k • written 5.6 years ago by ★ 2.6k
6
votes
14
replies
7.4k
views
Display pairwise p values on barplots in ggplot2
R ggplot2 barplot
updated 5.6 years ago by 43k • written 5.6 years ago by ★ 2.6k
1
vote
6
replies
4.5k
views
Trimmomatic only for removing adapters
trimmomatic RNA-Seq
updated 5.7 years ago by ▴ 80 • written 5.9 years ago by ★ 2.6k
2
votes
4
replies
1.5k
views
phred scores and mapping
Phred score mapping
updated 5.7 years ago by 20 • written 5.8 years ago by ★ 2.6k
2
votes
3
replies
1.5k
views
Conflict of abundances on different taxonomic levels using centrifuge
metagenomics centrifuge
updated 5.7 years ago by 6.5k • written 5.7 years ago by ★ 2.6k
0
votes
7
replies
1.3k
views
randomreads.sh simulated reads dont map to genome
bbmap
5.8 years ago by grant.hovhannisyan ★ 2.6k
2
votes
8
replies
1.2k
views
randomreads.sh simulated mates are far away
bbmap
updated 5.8 years ago by 35k • written 5.8 years ago by ★ 2.6k
3
votes
8
replies
1.2k
views
write total number of elements within labels of Venn diagram
R venn.diagram
5.8 years ago by grant.hovhannisyan ★ 2.6k
5
votes
3
replies
2.6k
views
paired-end reads in BBMap randomreads.sh
randomreads BBMap
updated 5.8 years ago by 142k • written 5.8 years ago by ★ 2.6k
9
votes
10
replies
6.0k
views
8 follow
Compare sets of GO enrichments
GO
updated 5.9 years ago by ★ 2.2k • written 6.1 years ago by ★ 2.6k
7
votes
10
replies
10k
views
Extract gene names from a particular cluster from pheatmap
pheatmap cluster R
6.0 years ago by grant.hovhannisyan ★ 2.6k
2
votes
3
replies
2.6k
views
remove sequences with non-canonical nucleotides from fasta file
SeqIO fasta
updated 6.2 years ago by ★ 2.1k • written 6.2 years ago by ★ 2.6k
3
votes
2
replies
1.8k
views
Stringtie/Cufflinks with yeast RNAseq
RNA-Seq Stringtie Cufflinks gffcompare cuffcompare
6.3 years ago by grant.hovhannisyan ★ 2.6k
6
votes
6
replies
13k
views
Read counts of STAR with gff file
read-counts gff STAR
6.3 years ago by grant.hovhannisyan ★ 2.6k
0
votes
1
reply
1.2k
views
Cufflinks reports less transcripts then in gff
cufflinks
6.3 years ago by grant.hovhannisyan ★ 2.6k
3
votes
5
replies
2.0k
views
simulate rnaseq reads from ref. genome
RNA-Seq simulation bbtools
updated 6.4 years ago by 142k • written 6.4 years ago by ★ 2.6k
8
votes
8
replies
6.1k
views
STAR for bacterial genome
STAR prokaryots
updated 2.7 years ago by • 0 • written 6.5 years ago by ★ 2.6k
0
votes
1
reply
3.0k
views
problems with updating deseq2
DESeq2 R Rstudio
6.5 years ago by grant.hovhannisyan ★ 2.6k
1
vote
9
replies
2.9k
views
DESeq2 with subset of genes
RNA-Seq DESeq2 hybrid
6.5 years ago by grant.hovhannisyan ★ 2.6k
1
vote
10
replies
2.4k
views
IGV with subset of bam file
IGV bam
6.6 years ago by grant.hovhannisyan ★ 2.6k
44
votes
34
replies
13k
views
7 follow
Technical replicates in RNAseq
RNA-Seq technical_replicates
2.2 years ago by grant.hovhannisyan ★ 2.6k
1
vote
5
replies
1.8k
views
Seq. depth for DE analysis
DE-analysis RNA-Seq
updated 13 months ago by 43k • written 6.6 years ago by ★ 2.6k
13
votes
9
replies
3.4k
views
number of genes in human genome
gene_id Ensembl
updated 6.6 years ago by 23k • written 6.6 years ago by ★ 2.6k
4
votes
7
replies
1.4k
views
ChipSeq multiplexing the number of TF
chipseq TF
updated 6.6 years ago by 104k • written 6.6 years ago by ★ 2.6k
1
vote
2
replies
4.6k
views
predict TF binding sites from DNA sequence
TF TRANSFAC TFBS binding-site
updated 16 days ago by 43k • written 6.7 years ago by ★ 2.6k
2
votes
3
replies
1.6k
views
reverse_complement on mutated sequence Biopython
biopython reverse_complement
updated 6.7 years ago by 11k • written 6.7 years ago by ★ 2.6k
4
votes
8
replies
2.3k
views
DESEQ2 for ASE
Allele-specific expression RNA-Seq DESEQ2
6.8 years ago by grant.hovhannisyan ★ 2.6k
54 results • Page 1 of 2
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