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121,965 results • Page 209 of 2440
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2.0k
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DESEq2 results : low counts too many genes
RNA-seq differential-expression deseq2
updated 2.0 years ago by 45k • written 2.1 years ago by ▴ 10
2
votes
3
replies
1.0k
views
Searching a tool to modify annotation files.
annotation
24 months ago by Charles Plessy ★ 2.9k
0
votes
1
reply
655
views
Geo2r rna seq analysis
Geo2r RNA-seq
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
2
votes
5
replies
1.5k
views
Extract only insecta information from Blast nr DB.
Blast
updated 2.1 years ago by 154k • written 2.1 years ago by • 0
2
votes
3
replies
1.7k
views
What is the fastest nucleotide sequence alignment search tool for 100mer queries versus a 2G database for nearly similar matches
alignment read nucleotide aligner sequence
updated 2.1 years ago by 154k • written 2.1 years ago by ▴ 60
1
vote
4
replies
2.6k
views
GEO dataset extraction
ncbi geo
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
1
vote
0
replies
512
views
Genes in open chromatin region
ATAC-seq DiffBind
2.1 years ago by Chris ▴ 360
3
votes
2
replies
832
views
HISAT2 Error
HISAT2
updated 2.1 years ago by 154k • written 2.1 years ago by ▴ 20
1
vote
0
replies
1.0k
views
Job: AstraZeneca funded PhD studentship: expanding the toolbox of molecular degraders through systematic degron discovery
machine-learning alphafold proteins
updated 24 months ago by 45k • written 2.1 years ago by ▴ 230
0
votes
1
reply
670
views
Issues while running BaseRecalibrator
BaseRecalibrator WGS
updated 2.1 years ago by 56k • written 2.1 years ago by ▴ 10
0
votes
1
reply
815
views
how do i convert my genomic data into proteome?
proteome data
updated 2.1 years ago by ★ 30k • written 2.1 years ago by • 0
0
votes
0
replies
515
views
MaxEntScan Alternative splice site prediction
MaxEntScan
2.1 years ago by Akshita • 0
0
votes
1
reply
866
views
how to calculate TM-score to p-value?
tmscore pdb protein structure
updated 2.0 years ago by • 0 • written 2.1 years ago by ▴ 80
2
votes
1
reply
907
views
Reducing BWA mem seed length when a genome is highly heterozygous?
alignment bwa
updated 23 months ago by 20k • written 2.1 years ago by ▴ 80
2
votes
1
reply
984
views
Producing Bulk samples from 10X data
rnaseq scrnaseq deseq2 bulk seurat
updated 2.1 years ago by 89k • written 2.1 years ago by ▴ 940
0
votes
2
replies
941
views
How to load a galaxy DESeq results table into R so I can continue my workflow there
r RNA-seq deseq2
2.1 years ago by Nicolas • 0
0
votes
1
reply
719
views
TCGAbiolinks MSI data
msi
updated 2.1 years ago by ★ 3.1k • written 2.1 years ago by ▴ 10
0
votes
0
replies
696
views
News: Course - RNAseq in non-model organisms
R Differential-Expression-Analysis RNA-seq Bioconductor
updated 24 months ago by 45k • written 2.1 years ago by ★ 2.6k
0
votes
2
replies
1.4k
views
Gene Ontology - How to do Transcript Ontology?
gene-ontology GO transcripts
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
1
vote
3
replies
1.5k
views
trajectory-like graph for a data frame
trajectory rna-seq tidyverse r velocity
updated 2.1 years ago by ★ 19k • written 2.1 years ago by ★ 1.9k
0
votes
11
replies
2.2k
views
Normalization for microarrays >1000+ samples?
microarray normalization oligo
2.0 years ago by evmae • 0
0
votes
0
replies
704
views
R crash when running leiden algorithm
seurat
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 360
4
votes
7
replies
4.7k
views
Corrupted FASTq files with missing "+" under some sequences.
fastq RNAseq corruption recover
updated 2.1 years ago by • 0 • written 4.4 years ago by ▴ 120
0
votes
3
replies
1.1k
views
RSubread DESeq2
RNA-seq subread differential-expression deseq2
updated 2.0 years ago by 45k • written 2.1 years ago by • 0
0
votes
0
replies
504
views
Fastest way to find private SNPs for each sample
SNP
2.1 years ago by Axzd ▴ 80
1
vote
8
replies
2.2k
views
NCBI Gene Table Bulk Download
ncbi gene_table
updated 2.1 years ago by 154k • written 2.1 years ago by • 0
0
votes
0
replies
541
views
simuations with sim1000g
snps simulation sim1000G chromosome
2.1 years ago by Eliza ▴ 30
0
votes
2
replies
1.9k
views
STAR mapping two pass mode for multiple samples with split steps or one step ?
STAR RNA-seq
2.1 years ago by octpus616 ▴ 120
0
votes
1
reply
780
views
Any alternatives to DrugBank?
DrugBank
updated 2.1 years ago by 154k • written 2.1 years ago by • 0
0
votes
0
replies
502
views
Coverage of domains
hmmer protein domains
2.1 years ago by unknownunknown • 0
0
votes
3
replies
1.3k
views
Seeking Assistance for Interpreting a Network Representation on String-DB.org
gene-ontology GO enrichment Proteome stringdb
updated 2.1 years ago by ★ 1.6k • written 2.1 years ago by ▴ 70
2
votes
1
reply
1.3k
views
Consensus Cluster takes normalized gene counts or raw gene counts?
R Gene-Expression ConsensusCluster DGE
updated 2.1 years ago by ★ 3.1k • written 2.1 years ago by ▴ 110
0
votes
1
reply
703
views
How to predict/annotate whether some type strains has a certain type of enzyme?
genome gene blast annotation
updated 2.1 years ago by 154k • written 2.1 years ago by • 0
0
votes
0
replies
632
views
TCGAbiolinks not working anymore
R TCGAbiolinks GDC
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
0
votes
0
replies
548
views
weird TLEN
bowtie2 samtools
updated 2.1 years ago by 154k • written 2.1 years ago by • 0
1
vote
3
replies
1.3k
views
RefseqID to gene symbol for multiple species
RefSeq Gene-Symbol
2.1 years ago by Jacob • 0
1
vote
1
reply
631
views
GISTIC CNV
Gistic
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
0
votes
0
replies
537
views
ClusterProfiler EMAP plot - what are the annotations?
clusterprofiler emap
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 20
5
votes
4
replies
1.4k
views
6 follow
How to delete part of row names in a list in linux
Linux
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
1
vote
1
reply
776
views
Long read filtering based on reference
Long-read ONT
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
2
votes
2
replies
1.0k
views
Tool: Python and R without installing apps
Resources
updated 2.1 years ago by ▴ 330 • written 2.1 years ago by ▴ 20
0
votes
4
replies
7.7k
views
PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset
tcga RNA-Seq gdc ebplusplus
updated 2.1 years ago by • 0 • written 6.7 years ago by ▴ 80
0
votes
0
replies
554
views
Tool: MTMCSKAT package for GWAS with efficient resampling, parallelization
SKAT MTMC-SKAT
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 100
0
votes
3
replies
1.1k
views
Not all variants are annotated with AF - expected or a problem?
Variant-Calling WGS Alignment
updated 18 months ago by 45k • written 2.1 years ago by ▴ 30
1
vote
2
replies
1.3k
views
Converting scMultiome data to loom using SEURAT
scMultiome CCAF Seurat
2.1 years ago by halimaakhter014 • 0
6
votes
6
replies
3.9k
views
Help with error scanpy
scanpy
updated 20 months ago by • 0 • written 2.1 years ago by ▴ 360
1
vote
2
replies
1.1k
views
Restricting vcf entries based on ID length
bcftools vcf vcftools
updated 2.0 years ago by 11k • written 2.1 years ago by • 0
3
votes
2
replies
2.3k
views
Could not view/find meta.data and Error merging three seurat object
Seurat single-cell
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 120
0
votes
2
replies
917
views
Sentrix Array Genotyping
Illumina
2.1 years ago by joo • 0
0
votes
0
replies
551
views
Help with scvi error
scvi
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 360
121,965 results • Page 209 of 2440
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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
A: GATK ASEReadCounter: Downstream analysis for identifying allele specific express
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Recent Replies
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…
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
Yes it does not match at all, and those genes that are common in both analysis results have very different logFC and p values
Comment: Errors with RSEM/bowtie2 by Olivia • 0
I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
Answer: Gene expression equivalent of polygenic risk score ? by GouthamAtla 12k
I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
Comment: ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues usin by Ben • 0
write.table(df1, "df1.txt", sep = "\t", row.names = T, col.names = T, quote = FALSE)
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