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1,104 results • Page 3 of 23
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6
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8
replies
549
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BRAKER3 genome annotation
annotation BRAKER3 genome
updated 10 days ago by 14k • written 12 days ago by ▴ 40
0
votes
8
replies
325
views
Error in cnetplot enrichplot package
R
updated 4 days ago by 43k • written 4 days ago by • 0
3
votes
8
replies
1.3k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 7 days ago by 14k • written 9 months ago by ▴ 80
4
votes
8
replies
448
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 8 hours ago by 35k • written 1 day ago by ▴ 10
2
votes
7
replies
5.7k
views
8 follow
How to access specifically 30x NA12878 sequencing runs
giab benchmark fastq wgs data-access
updated 24 days ago by ▴ 360 • written 5.1 years ago by • 0
4
votes
7
replies
4.5k
views
snakemake output directory
snakemake ngs
updated 11 days ago by • 0 • written 3.9 years ago by ▴ 200
4
votes
7
replies
593
views
UK biobank versus Genomics England
WGS DRAGEN GenomicsEngland UK-BRAP vcf
written 12 weeks ago by ★ 4.3k
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 10 days ago by • 0 • written 6 months ago by ▴ 50
0
votes
7
replies
313
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 20 hours ago by 141k • written 4 days ago by • 0
0
votes
7
replies
405
views
DESeq: too low p-value for RNAseq
R DESeq p-value RNA-seq FDR
updated 22 days ago by ★ 2.9k • written 23 days ago by ▴ 10
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 18 days ago by 43k • written 3.7 years ago by ▴ 20
2
votes
7
replies
512
views
STARsolo ; Reads are NOT mapped to transcriptome
STARsolo
updated 16 days ago by 141k • written 17 days ago by • 0
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 1 day ago by ▴ 850 • written 6.1 years ago by ▴ 10
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 11 days ago by • 0 • written 9.2 years ago by ▴ 970
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 10 days ago by 43k • written 7.6 years ago by ▴ 70
7
votes
7
replies
1.2k
views
Forum: Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career advice
updated 11 days ago by ★ 2.5k • written 12 days ago by • 0
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering dendrogram RNA-Seq batch-effect
updated 8 days ago by 43k • written 4.0 years ago by ▴ 500
4
votes
7
replies
502
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 6 hours ago by ★ 5.8k • written 4 days ago by ▴ 10
3
votes
7
replies
964
views
How much adapters is it ok to keep in my samples after RNA seq?
RNA-seq illumina adapters
updated 22 days ago by 43k • written 5 months ago by ▴ 150
1
vote
7
replies
5.1k
views
How do I plot several sns.clustermap heatmaps in a single figure?
python seaborn
updated 16 days ago by ▴ 40 • written 3.4 years ago by ▴ 880
3
votes
7
replies
460
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq tmt nomenclature proteomics
10 days ago by ntsopoul ▴ 60
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 17 days ago by 43k • written 6.4 years ago by ▴ 10
3
votes
7
replies
523
views
Artificial deletion in bam
bam
updated 21 days ago by ★ 1.2k • written 22 days ago by ▴ 10
0
votes
7
replies
476
views
Selection criteria for nanobody
Nanobody
updated 25 days ago by 3.9k • written 26 days ago by • 0
1
vote
7
replies
15k
views
7 follow
How To Annotate Methylation 450K?
methylation
updated 22 days ago by • 0 • written 10.1 years ago by ▴ 210
4
votes
7
replies
426
views
To get p-values for the TPM
P-value TPM RSEM
updated 2 days ago by ★ 5.8k • written 3 days ago by • 0
1
vote
7
replies
468
views
Installing Cell Ranger
cellranger
24 days ago by gdfsnkfns • 0
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 9 days ago by 43k • written 4.3 years ago by ▴ 360
7
votes
7
replies
554
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein pdb protein-databank
updated 14 days ago by 4.5k • written 14 days ago by • 0
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 7 days ago by 82k • written 7.2 years ago by ▴ 80
2
votes
7
replies
5.1k
views
9 follow
problem with HOMER findMotifsGenome.pl
HOMER ATAC-Seq
updated 16 days ago by • 0 • written 5.6 years ago by ▴ 80
4
votes
7
replies
555
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 13 days ago by 43k • written 14 days ago by ▴ 20
0
votes
7
replies
653
views
Help with summarizeOverlaps function in RNASeq analysis using R
R RNA-Seq summarizeOverlaps GenomicAlignments
updated 19 days ago by ★ 1.7k • written 28 days ago by • 0
1
vote
7
replies
438
views
fastp - can I trim specific adapters only?
trimming fastp adapter
16 days ago by liorglic ★ 1.4k
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 8 days ago by 43k • written 4.9 years ago by ▴ 140
2
votes
7
replies
822
views
Removing duplicates
duplicates ONT minimap2
updated 8 days ago by ▴ 510 • written 10 days ago by • 0
4
votes
7
replies
566
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 25 days ago by ★ 3.8k • written 28 days ago by ▴ 140
5
votes
6
replies
398
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot RNAseq Rstudio
updated 24 days ago by 100k • written 25 days ago by • 0
7
votes
6
replies
478
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
5 days ago by analyst ▴ 30
1
vote
6
replies
423
views
Rename multiple fastq.gz files
fastq next-gen
updated 10 days ago by 8.4k • written 10 days ago by • 0
2
votes
6
replies
1.8k
views
7 follow
DNA methylation preprocessing
SWAN DNA methylation Funnorm
updated 13 hours ago by 43k • written 2.4 years ago by ▴ 10
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq batch-effect
updated 9 days ago by 43k • written 4.8 years ago by ▴ 30
2
votes
6
replies
863
views
Batch effect correction with cell type enrichment analysis
limma RNA-seq r batch-effect
updated 10 days ago by 43k • written 19 months ago by ▴ 140
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 17 days ago by 43k • written 5.5 years ago by ▴ 100
4
votes
6
replies
448
views
Odd results with BLAST remote
blast remote NCBI
updated 11 days ago by ▴ 170 • written 12 days ago by ▴ 150
2
votes
6
replies
5.2k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq R seurat harmony batch-effect
updated 8 days ago by 43k • written 3.7 years ago by • 0
0
votes
6
replies
316
views
How to slice a gvcf file with tabix?
Tabix bed gvcf
3 days ago by Sd • 0
2
votes
6
replies
3.6k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 1 day ago by 82k • written 3.9 years ago by ▴ 280
9
votes
6
replies
1.5k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr amplicon primer
updated 24 days ago by 43k • written 16 months ago by ▴ 710
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray r GEOquery
updated 10 days ago by 43k • written 5.0 years ago by ▴ 30
1,104 results • Page 3 of 23
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Answer: Is there a tool that sorts gtf files?
Answer: gvcf joint calling
Answer: Heatmap and rna-seq
Answer: How to use limma to find differentially expressed genes in response to a continu
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A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
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Comment: ScRNA data question by starswillfade ▴ 10
features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
Comment: gvcf joint calling by zihanss • 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
Comment: Correct way to compare multiple treaments between RNA-Seq samples using edgeR? by Guille • 0
Thank you for your answer! The MDS plot seems to group most treatment groups close-by, so I'm starting to suspect the effect of treatment …
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC: by Mensur Dlakic ★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq by dsull ★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
Answer: Limma Analysis Agilent Microarray Data (GPL1708) by Gordon Smyth ★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR? by Gordon Smyth ★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu by Gordon Smyth ★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing by cao510927 ▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Alex Reynolds 35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data by bk11 ★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq by GenoMax 141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq by dsull ★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
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