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101
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19
replies
38k
views
19 follow
Tutorial: Heatmaps in R
heatmap R
updated 11 months ago by ▴ 70 • written 9.1 years ago by 27k
0
votes
1
reply
1.3k
views
Position of Scale bar
ggplot2
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Forum: Phylogenomic study: suggestions and tips
evolution species genus phylogenomic phylogenetics
4.4 years ago by tiagobellintani ▴ 40
2
votes
2
replies
1.3k
views
paired reads have different names
BWA
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Predicting Drug responds from somatic mutations
prediction somatic responds drug
updated 4.4 years ago by ▴ 580 • written 4.4 years ago by ▴ 420
5
votes
9
replies
13k
views
6 follow
ANOVA for RNA-seq data?
anova RNA-Seq
updated 4.0 years ago by 9.0k • written 5.8 years ago by ▴ 120
0
votes
2
replies
2.0k
views
Batch effects and differential expression analysis on TCGA data for cancer subtypes
RNA-Seq TCGA batch
4.4 years ago by antmantras ▴ 80
7
votes
6
replies
7.5k
views
How to create SAF from text file for FeatureCounts
featureCounts ATAC-seq
updated 13 months ago by ▴ 80 • written 4.4 years ago by ▴ 70
0
votes
1
reply
984
views
update fasta header and gff3 file
fasta gff awk header python
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by ▴ 10
0
votes
1
reply
2.3k
views
Greengenes homepage
Greengenes
updated 4.4 years ago by 35k • written 4.4 years ago by ▴ 340
2
votes
5
replies
1.8k
views
Use Rfam to remove contaminants from miRNA-seq
Rfam miRNA contaminant sequensing
updated 4.4 years ago by 22k • written 4.4 years ago by ▴ 20
0
votes
0
replies
1.1k
views
dynamic input/output in the snakemake rules
RNAseq Snakemake dynamic bam
4.4 years ago by ali • 0
2
votes
2
replies
1.5k
views
SNP count in a set of genomic regions
annotations SNPs 1000G
updated 4.4 years ago by 14k • written 4.4 years ago by ▴ 90
50
votes
17
replies
42k
views
17 follow
How To Get Number Of Reads In Bam File Efficiently In Python?
python samtools next-gen sequencing
updated 2.9 years ago by 45k • written 15.2 years ago by ▴ 840
0
votes
0
replies
677
views
average variants number human WGS
variant WGS SNP INDEL
4.4 years ago by cocchi.e89 ▴ 290
1
vote
1
reply
1.3k
views
two allele frequency
allele position BCFTOOLS
updated 4.4 years ago by 14k • written 4.4 years ago by ▴ 110
0
votes
0
replies
590
views
How to average DESeq2’s median of ratios from replications
Deseq2
4.4 years ago by yosapol.harn • 0
0
votes
3
replies
1.5k
views
Cellular deconvolution intuition
deconvolution
4.4 years ago by Aspire ▴ 390
0
votes
1
reply
574
views
how to use python to only read sequences from fasta files
sequencing python genome fasta
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 10
0
votes
0
replies
699
views
Freebayes - too many variants produced on WES sample
Freebayes
4.4 years ago by esimonova.me ▴ 30
0
votes
1
reply
927
views
Bash Script for a specific SNP
SARS-CoV-2 BASH SNPS
updated 4.4 years ago by 153k • written 4.4 years ago by • 0
0
votes
3
replies
1.2k
views
RefSeq assession IDs
RefSeq Gene
4.4 years ago by chaochao ▴ 20
0
votes
0
replies
853
views
how to downlaod parkinson's disease GWAS summary statistics file
GWAS
4.4 years ago by BenHu • 0
0
votes
2
replies
2.0k
views
Error while plotting heatmap
heatmap RStudio
4.4 years ago by mrinsmrids • 0
1
vote
1
reply
636
views
Differential expression analysis using SCAN data
differential-expression
updated 4.4 years ago by 89k • written 4.4 years ago by • 0
0
votes
1
reply
4.7k
views
simplify function on enricher output of ClusterProfiler
clusterProfiler
updated 4.4 years ago by ▴ 20 • written 6.5 years ago by • 0
0
votes
1
reply
928
views
Conflict result between RNA-seq and Western-Blot
RNAseq protein
updated 4.4 years ago by ★ 3.1k • written 4.4 years ago by ★ 9.6k
0
votes
0
replies
792
views
Why do I keep encountering the following errors whenever I run the naccess program to calculate the interface area of a protein with multiple chains?
Naccess Interface-area PDB PPI
4.4 years ago by Cm • 0
0
votes
0
replies
652
views
Single Factor Design and Dispersion and BCV
bcv dispersion edegr
4.4 years ago by plewis8 • 0
0
votes
0
replies
674
views
clarification about WGA (Whole genome Amplification)
sample library NGS
4.4 years ago by Ruolin Liu • 0
1
vote
7
replies
3.2k
views
many intronic reads and no features counts in 3' RNA-seq sequencing
RNA-Seq
updated 4.4 years ago by ▴ 80 • written 5.6 years ago by ▴ 10
5
votes
6
replies
2.9k
views
Error in library(preproc) : there is no package called ‘preproc’
metaOmics R Packages Rstudio
4.4 years ago by xxxxxxxx ▴ 20
0
votes
3
replies
2.9k
views
Allele Specific Expression (ASE) from RNA seq data
AlleleSpecificExprssion ASEReadCounter RNAseq
updated 4.4 years ago by ▴ 720 • written 4.4 years ago by ▴ 140
0
votes
1
reply
1.6k
views
To construct the Venn diagram from Roary
roary pangenome venn
updated 4.4 years ago by • 0 • written 4.5 years ago by • 0
0
votes
0
replies
670
views
Simulated data or pseudoreplicatesreported in papers
pseudoreplicates SNPs INDELs
4.4 years ago by esimonova.me ▴ 30
0
votes
0
replies
1.8k
views
Job: Research Scientist at Lausanne, Swiss Institute of Bioinformatics
nash omics SIB research
4.4 years ago by Rishika • 0
0
votes
2
replies
956
views
Gene ontology analysis
enrichment methylation gene_identifier
4.3 years ago by Kajol • 0
0
votes
0
replies
2.0k
views
grouping in EdgeR
EdgeR RNA-SEQ
4.4 years ago by BDK_compbio ▴ 140
0
votes
2
replies
1.2k
views
DESEQ2
featurecount DeSeq2
4.4 years ago by rheab1230 ▴ 150
0
votes
1
reply
746
views
What type of statistical study can I can conduct based on data obtained
r statistics
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 10
0
votes
0
replies
840
views
Job: Positions at the Penn Epigenetics Institute
computational-biology epigenetics
updated 2.5 years ago by 45k • written 4.4 years ago by • 0
2
votes
3
replies
6.6k
views
10x scRNA-Seq Multiplet Calculations
doublet multiplet 10x scRNA-Seq QC
4.3 years ago by Charles Warden 8.3k
0
votes
4
replies
1.3k
views
Transcription factor
RNA-seq analysis
4.4 years ago by rheab1230 ▴ 150
0
votes
0
replies
921
views
Job: Postdoc position in computational population genetics
populationgenetics ancientdna postdoc
4.4 years ago by Gabriel R. ★ 2.9k
2
votes
4
replies
2.8k
views
bedGraphToBigWig
Seq ChIP
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 170
0
votes
0
replies
1.0k
views
snpEff gives warning: INFO_REALIGN_3_PRIME, what does it mean?
annotation vep snpeff
4.4 years ago by boxate1618 ▴ 60
1
vote
1
reply
1.4k
views
scRNA-Seq GEX 5' v1.0 High Cell Count with Low Gene Count
10x scRNA-seq downsampling
4.4 years ago by tdfyoder ▴ 40
1
vote
5
replies
2.1k
views
Memory Error
R Memory MOFA
updated 4.4 years ago by ★ 2.9k • written 4.4 years ago by ▴ 110
3
votes
5
replies
2.1k
views
metaOmics Installation issues in windows 4.0.5 using R
metaOmics R meta-analysis R-studio
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 20
0
votes
1
reply
1.3k
views
How to find single copy genes from OrthoFinder output
singlecopygenes Orthofinder
updated 4.4 years ago by ★ 2.9k • written 4.4 years ago by • 0
121,894 results • Page 661 of 2438
Recent Votes
Comment: Best way to do protein structure guided similarity search?
Comment: Tool 'sra_source' does not exist.
Answer: TCGA -derived Large RangeSummarizeExperient file
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Answer: Structural Variant identification on pangenome graphs
Answer: Stringtie de novo VS reference guided (-G)
Answer: Yeast reference-based genome assembly
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Comment: Different UMAP for batch correction in R and Pytho by GenoMax 153k
Use this tutorial for how to upload images: https://www.biostars.org/p/309884/#346553 Only difference is instead of using an external imag…
Answer: GTEx sQTL v8 – annotation version used? by GenoMax 153k
If you click over to the `Reference` tab ( https://gtexportal.org/home/downloads/adult-gtex/reference ), it looks like they used GENCODE v.…
Comment: How to Identify Conserved 21-mers Across TE Insertions in Drosophila? by manikin_python9f ▴ 20
Since they are transposons, we don’t know the exact location of them. We know their sequence of insertions from repeatmasker in dm6 genome.…
Comment: Tool 'sra_source' does not exist. by Atefeh • 0
Thanks for your kindness.
Comment: TCGA -derived Large RangeSummarizeExperient file by Tom • 0
It works well. Thank you very much ! @atpoint
Answer: TCGA -derived Large RangeSummarizeExperient file by ATpoint 89k
For the end user these `DFrames` are just regular data.frames, so you can do `col_data[,c("barcode", "patient", "whatever")]` or just do `a…
Comment: magpurify errors by shevch2009 ▴ 20
I have checked with my eyes, and I didn't find it, I have only one contig that starts with k127_458 .... but the name is different - k127_4…
Comment: Yeast reference-based genome assembly by Michael 56k
So, you aren't sure about the exact species? Then you might want to be careful with reference-based assembly in general. I recommend the fo…
Comment: Structural Variant identification on pangenome graphs by Panos ★ 1.8k
That's a very comprehensive list! Thanks for sharing! `minigraph` better suits my needs because all I need is SVs for my genomes. As far a…
Comment: Yeast reference-based genome assembly by amy967107 • 0
I have ~2.01 Gb of ONT data and the target genome is ~20–23 Mb (90–100× coverage). My ONT read N50 is ~3.8 kb, so contiguity may be limited…
Comment: Yeast reference-based genome assembly by amy967107 • 0
This is a yeast strain (probably Rhodotorula spp.) and I'm trying to assemble the entire genome from nanopore reads using a reference-based…
Answer: Yeast reference-based genome assembly by Michael 56k
The new [hifiassm ONT][1] may be all you need for getting a good assembly. I would not recommend LRSDAY, except for its annotation part (wh…
Comment: magpurify errors by Mensur Dlakic ★ 30k
By the way, these errors are not unique. If you look through the `magpurify` GitHub issues, both types have been reported already. - https…
Comment: magpurify errors by Mensur Dlakic ★ 30k
There is absolutely no chance that a contig labeled `k127_4584534` doesn't exist in your fasta files. These names are not made up out of th…
Comment: magpurify errors by shevch2009 ▴ 20
Strange but there are no such headers or contig names in my fasta files
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