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Time-series RNA-seq analysis using DESeq2
RNA-Seq time-course LRT time-series DESeq2
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
1
vote
9
replies
4.4k
views
build databses for genome using snpEff
annotation SNP snpEff
updated 2.1 years ago by • 0 • written 7.2 years ago by • 0
1
vote
2
replies
900
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Tools To predict TSS(Transcription start sites ) in plant genomes ??
Prediction Annotation Plants TSS Genome
2.1 years ago by nikhil ▴ 20
14
votes
3
replies
21k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 2.1 years ago by ▴ 40 • written 8.5 years ago by ★ 1.6k
2
votes
1
reply
1.2k
views
IDAT or Txt MINFI or LIMMA?
Methylation
updated 2.1 years ago by ★ 3.1k • written 2.1 years ago by • 0
4
votes
7
replies
2.9k
views
Colabfold: predicting structure of homotrimer vs 3 linked units
colabfold alphafold
updated 2.1 years ago by ▴ 50 • written 2.1 years ago by ▴ 10
2
votes
5
replies
1.4k
views
vcf file
gwas Plink analysis
updated 2.1 years ago by 154k • written 2.1 years ago by ▴ 10
0
votes
0
replies
506
views
How to implement the code in MonkeyBread package
Visium spatial_transcriptomics MonkeyBread
2.1 years ago by piotto ▴ 20
1
vote
4
replies
1.9k
views
how to solve the problem "Invalid character (+) in sequence"
metagenome args_oap
2.1 years ago by alice005201314 • 0
1
vote
1
reply
952
views
How to remove the rownames in heatmap generated plot?
heatmap annotation
updated 2.1 years ago by ★ 3.1k • written 2.1 years ago by • 0
0
votes
1
reply
958
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DNA alignment strand
BLAST NCBI DNA alignment
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
1
vote
4
replies
2.6k
views
Retrieving single-cell dataset from GEO database
seurat GEO r single-cell
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 70
0
votes
2
replies
1.0k
views
Data quality on single nuclei transcriptomics
single transcriptomics quality nuclei Data
2.1 years ago by hema B • 0
2
votes
20
replies
4.6k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
2.1 years ago by Maxine ▴ 50
1
vote
1
reply
911
views
Bioinformatics Workflow
genetic-characterisation genetics genome-alignment
updated 2.1 years ago by ★ 19k • written 2.1 years ago by • 0
3
votes
3
replies
4.6k
views
Converting SAM to BAM files
chipseq
2.1 years ago by alphaflylizard • 0
0
votes
2
replies
798
views
Is chi-square test suitable for my categorical data?
statistics r
2.1 years ago by Apex92 ▴ 320
1
vote
3
replies
2.6k
views
EdgeR analysis of RNA-seq data in R for beginners using Ensembl ID
Ensembl edgeR
updated 2.1 years ago by ▴ 10 • written 2.1 years ago by • 0
5
votes
10
replies
2.5k
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR RNA-seq
2.1 years ago by alwayshope ▴ 40
2
votes
3
replies
1.4k
views
CNV benchmarking
CNV Benchmarking
updated 2.1 years ago by ★ 3.0k • written 2.1 years ago by ▴ 130
3
votes
2
replies
1.0k
views
Converting a bam dataset to vcf
bam vcf
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 40
0
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5
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1.5k
views
How to convert BigWig file to GCT File?
bigwig rna-seq gct
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 20
1
vote
3
replies
1.6k
views
Connecting to Web... problem in plink?
plink bed vcf
2.1 years ago by guntul ▴ 40
0
votes
1
reply
1.6k
views
Error with plot functions: Graphic API version mismatch
Vlnplot Seurat single-cell
updated 2.1 years ago by ★ 19k • written 2.1 years ago by • 0
0
votes
0
replies
965
views
Forum: I have a Master's and little experience in Bioinformatics - what would be the next best step?
career
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 10
0
votes
2
replies
1000
views
Testing Gene Set Overlap with Binomial Distribution or Hypergeometric Distribution
statistics Enrichment
2.1 years ago by Apex92 ▴ 320
0
votes
0
replies
765
views
GCP vertex AI errors
google-cloud-platform vertex-ai google-workflows
2.1 years ago by dthorbur ★ 3.1k
0
votes
0
replies
790
views
Principal component analysis (PCA) from Desmond output file
Desmond PCA prody Simulation
2.1 years ago by bhavya2269 • 0
3
votes
1
reply
1.0k
views
Extremely high ChIP-seq peak at mouse Chr2 "Gm10800" region
ChIPseq peak TF chipseq
updated 2.1 years ago by 89k • written 2.1 years ago by ▴ 30
0
votes
0
replies
506
views
molecular docking of thousands of proteins with a ligand
autodock-vina blind-docking
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
0
votes
0
replies
520
views
TSS prediction tools for plants
TSS-Prediction Plants TSS
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 20
3
votes
3
replies
1.1k
views
Over Representation Analysis over one specific pathway
GSEA DGE ORA
2.1 years ago by Manuel Sokolov Ravasqueira ▴ 110
2
votes
2
replies
1.5k
views
Nextflow: absolute file path gets concatenated?
nextflow
2.1 years ago by Eliveri ▴ 350
2
votes
4
replies
1.3k
views
Computing pairwise AA global sequence alignment between all pairs in a vector of sequences
pairwiseAlignment
2.1 years ago by rubic ▴ 270
1
vote
2
replies
1.6k
views
Align raw Nanopore reads (amplicon, long PCR)
Nanopore
2.1 years ago by garden_giessen ▴ 130
6
votes
1
reply
4.8k
views
How does FindNeighbors() and FindClusters() related and work?
seurat clustering
updated 2.1 years ago by ★ 3.1k • written 2.1 years ago by ▴ 150
3
votes
10
replies
2.8k
views
How to deal with duplicates between two database IDs?
Identifiers Database
2.1 years ago by benoahb ▴ 40
0
votes
0
replies
505
views
Pseudobulk model design: account for both capture and individuals hashed within capture?
pseudobulk linear-modeling DESeq2 RNA-seq
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 40
0
votes
2
replies
1.3k
views
efetch from NCBI E-utilities returns "curl error s 400 & 500" and takes a very long time
NCBI efetch E-utilities
2.1 years ago by Eugene • 0
2
votes
4
replies
1.8k
views
blastdbcmd error with -target_only option
blastdbcmd
2.1 years ago by biomarco ▴ 50
0
votes
0
replies
508
views
Assign gene to peak in bulk ATAC-seq
ATAC-seq
2.1 years ago by Chris ▴ 360
0
votes
1
reply
761
views
How to get MD tag sequence of a read from a sam file given a bed file?
samtools bed sam cigar
updated 2.1 years ago by ▴ 390 • written 2.1 years ago by • 0
1
vote
5
replies
2.5k
views
Questions about per base sequence quality and GC content.
fastqc fastq seq RNA
2.1 years ago by bioinfo ▴ 160
3
votes
2
replies
1.5k
views
GI numbers in NCBI
numbers GI NCBI
2.1 years ago by Christoph ▴ 30
1
vote
1
reply
1.5k
views
Spike-in normalization via deepTools multiBamSummary --scalingFactors: What's an appropriate --binSize?
spike-in ChIP-seq deepTools
updated 2.1 years ago by ★ 1.6k • written 2.1 years ago by ▴ 380
8
votes
5
replies
2.3k
views
What database would have a list of gene names and aliases for yeast?
yeast
updated 2.1 years ago by ★ 2.1k • written 2.1 years ago by ▴ 380
8
votes
2
replies
2.0k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 2.1 years ago by 45k • written 2.1 years ago by ★ 2.6k
10
votes
9
replies
8.4k
views
Conda/Mamba environment activation error
shell mamba conda wsl
updated 2.1 years ago by ▴ 880 • written 2.2 years ago by ▴ 240
2
votes
2
replies
2.4k
views
How to display gene expression after Harmony correction in scRNA-seq analysis
scRNA-seq correction Harmony
18 months ago by tujuchuanli ▴ 130
2
votes
2
replies
1.0k
views
Annotating gene function categorisation in r
gene r
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 10
121,966 results • Page 218 of 2440
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Answer: How to create a consensus of a contig with samtools or bbmap?
Comment: Getting just fastqc.zip file?
alternate allele frequency and minor allele frequency
Calculating minor allele frequency for GnomAD VCF file
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Answer: Gene expression equivalent of polygenic risk score ?
A: TRF output to .gff file
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Recent Replies
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
Have included the links to the papers I mentioned in another comment for reference!
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
These are the 2 papers I mentioned previously that used data other than raw counts for their analysis: https://onlinelibrary.wiley.com/doi/…
Answer: Collect COV file by BedCoverage by eshrakaali_p • 0
Hello German , I am using clinCNV for WES and i faced the same error and this part of the error [1] "ERROR: your file with normal coverage…
Comment: How to create a consensus of a contig with samtools or bbmap? by marongiu.luigi ▴ 760
sorry, I have mistaken samtools with spades... running `samtools view -h...` did the trick. Thank you.
Comment: Help with Ideathon by V K • 0
Thank you for the response! Unfortunately this is completely independent and not part of a course. I was asking for some innovative ways to…
Answer: How to create a consensus of a contig with samtools or bbmap? by lieven.sterck 16k
You assembled a genome using samtools ???? that sounds very weird, if not impossible ... The header (SQ lines) is missing from your file b…
Answer: gnomad par region variants by benformatics 4.2k
The XX and XY counts are present on any given variants page.
Comment: Help with Ideathon by Mensur Dlakic ★ 30k
I don't see a single question here. Saying `I need your expert help in figuring out how I can make this analysis useful!` is too open-ended…
Comment: Differences between published differential gene expression results and own analy by ATpoint 89k
Please link the paper, lets see their methods. With human data it can well be that they included something like surrogate variables to damp…
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
There are many ways to do normalization and one of the correct ways is simply to plug raw counts into deseq2 (the math that deseq2 uses to …
Comment: tximport error (medianLengthOverIsoform) by rfran010 ★ 1.6k
Is it the version number in your data? e.g. ENST00000415118.1 vs ENST00000415118 could be causing the mismatch?
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
So is there any correct way for normalisation? I know limma recommends CPM via limma-voom and DESeq2 just takes in raw counts and does thei…
Comment: Gene expression equivalent of polygenic risk score ? by Picasa ▴ 690
Thanks a lot for your answer. I will check the paper.
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
If those logFCs are different, then that's a normalization issue. The logFC is straight forward arithmetic (it's simply dividing mean of […
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
Thanks both for your input. It got me to look at the published methodologies more closely, and you guys were right. One paper that I was re…
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