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2
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1.5k
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NIPT related tools & software
NIPS
4.3 years ago by smrutimayipanda ▴ 20
14
votes
3
replies
7.6k
views
TMM-Normalization
TMM RNAseq-Normalization
3.9 years ago by Filago ▴ 110
0
votes
0
replies
783
views
How to annotate variants against hs37d5?
SNP annotation
4.4 years ago by vinayjrao ▴ 260
1
vote
2
replies
1.2k
views
genomicdbImport issue
genomicdbImport gatk
4.3 years ago by ijlal.hyder2012 ▴ 20
0
votes
3
replies
1.7k
views
Skewed Betweenness Centrality values resulting in almost unusable PPI networks for my university project - what can I do?
Cytoscape
updated 4.2 years ago by 45k • written 4.4 years ago by ▴ 20
0
votes
0
replies
768
views
How to sort and rank compounds docked with AutoDock Vina when the result is presented as only single decimal number?
Docking autodockVina VS VirtualScreening
4.4 years ago by srdjanmasirevic2 ▴ 20
0
votes
1
reply
1.9k
views
RagTag assembly after spades
spades conting ragtag scaffolds
updated 4.4 years ago by ▴ 600 • written 4.4 years ago by ▴ 10
9
votes
4
replies
14k
views
Installing perl modules on a conda environment produce changes out of the environment?
conda perl
updated 4.4 years ago by 8.9k • written 4.4 years ago by ▴ 140
1
vote
0
replies
933
views
Codon alignment with degenerate nucleotides?
paml codeml codon alignment
4.4 years ago by DNAlias ▴ 40
3
votes
1
reply
5.6k
views
add patient information to the metadata or Make New Orig.ident in seurat object
R RNA-SEQ Seurat
4.4 years ago by Maria17 ▴ 40
2
votes
3
replies
1.6k
views
RNAseq
stringtie rnaseq error gffcompare
4.4 years ago by mtavakoli4030 ▴ 10
1
vote
2
replies
2.8k
views
Duplicated Gene Symbol names after geneID conversion
geneID
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 70
1
vote
1
reply
1.3k
views
How to merge two GTFs which share some common features
stringtie GTF annotation
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 40
0
votes
0
replies
1.0k
views
my gffcompare out put gtf file is like that. on complete row is followed by some uncomplete row wich have not class codes.
gffcompare rna lncrna gtf
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 10
1
vote
1
reply
1.1k
views
Performance metrics of aligners and variant callers
benchmarking WGS
updated 4.4 years ago by 23k • written 4.4 years ago by ▴ 10
2
votes
2
replies
1.5k
views
News: Bioinformatics Solutions on AWS
Cloud AWS
updated 4.2 years ago by 45k • written 4.4 years ago by ▴ 20
9
votes
13
replies
3.3k
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq DESeq2
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 30
2
votes
2
replies
1.9k
views
making a PCA from MASH distance result
MASH R PCA
4.4 years ago by v.berriosfarias ▴ 140
0
votes
0
replies
662
views
Query on miRDeep2
mirDeep2 mapper
updated 4.4 years ago by 5.8k • written 4.4 years ago by • 0
3
votes
2
replies
2.4k
views
Negative values in Cox regression analysis
survival CoxPH coxregression
4.4 years ago by Amir.Asgary ▴ 30
1
vote
2
replies
1.4k
views
bedtool closest
bedtools
updated 2.2 years ago by 45k • written 4.4 years ago by ▴ 10
3
votes
3
replies
1.9k
views
Visualize DNA sequence as a dot plot?
plot visualization DNA dot
updated 4.4 years ago by 36k • written 4.4 years ago by • 0
0
votes
0
replies
869
views
How should we replace NAs from a genelight object?
R glpca adegenet GBS SNP
4.4 years ago by jaafari.omid ▴ 80
1
vote
1
reply
1.1k
views
Protein-Protein interaction for Upregulated genes
STRING DEGs PPI
updated 4.4 years ago by ★ 30k • written 4.4 years ago by ▴ 20
1
vote
2
replies
1.3k
views
Geno Ontology Analysis
GO hypergtest
updated 4.4 years ago by 35k • written 4.4 years ago by ▴ 20
4
votes
2
replies
1.9k
views
How to retrieve protein sequence from gene ID and output a fasta file
ncbi gene protein biopython entrez
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 10
0
votes
0
replies
720
views
drug resistance informations for variations
cosmic somatic drug variants germline
4.4 years ago by enes ▴ 40
0
votes
3
replies
1.6k
views
DiffBind consensus peak extraction
DiffBind ChIP-seq
updated 4.4 years ago by ★ 2.1k • written 4.4 years ago by • 0
3
votes
2
replies
2.3k
views
hisat2 output from paired en reads.
hisat2 rna-seq
updated 4.4 years ago by ★ 2.2k • written 4.4 years ago by ▴ 140
5
votes
2
replies
2.8k
views
GATK variant annotation
vcf gatk
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 40
0
votes
0
replies
791
views
Assembly pipeline/tutorial for SMRT (PacBio) sequenced bacterial genome data?
python perl pipeline genome sequence
4.3 years ago by Kumar ▴ 120
0
votes
0
replies
673
views
MACS2 Summit TSSPlot dividing BDG into bins
TSS Callpeaks MACS2
4.4 years ago by Seigfried ▴ 80
0
votes
0
replies
2.9k
views
Include - in part of the motif for analysis? And "It looks like we don't support this file format" when opening weblogo motif
motif aminoacids sequence biopython weblogo
4.4 years ago by minifoog ▴ 10
0
votes
0
replies
833
views
LD score regression of data including SNPs with extremely low P-value
heritability SNP LDSC
4.4 years ago by Apprentice ▴ 190
0
votes
1
reply
842
views
gRNA concatamer - will it work ?
gRNA CRISPR PAM
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 10
0
votes
0
replies
1.0k
views
Job: Bioinformatician/Programmer at the University of Pennsylvania
pipelines programmer bioinformatician python r
4.4 years ago by adamnaj • 0
0
votes
0
replies
907
views
Job: Bioinformatician at Turbine / Hungary
proteomics cancerreserach singlecell python r
4.4 years ago by timea.volenter • 0
0
votes
0
replies
1.0k
views
panel of normals for mutect2
mutect2 gatk NGS PoN somatic
4.4 years ago by lait ▴ 180
0
votes
2
replies
3.0k
views
format conversion using OpenBabel
software
4.4 years ago by roybatty269 • 0
1
vote
2
replies
1.1k
views
Program for predicting RNA sequences that may bind to a protein Domain
protein Binding domain RNA
updated 4.4 years ago by ★ 30k • written 4.4 years ago by ▴ 80
4
votes
6
replies
7.5k
views
Understanding TCGA's ASCAT copy number data
tcga ascat copy number
updated 4.2 years ago by 89k • written 4.5 years ago by ▴ 90
0
votes
1
reply
992
views
GDC Data Query
RNA-Seq
updated 4.4 years ago by ★ 1.3k • written 4.5 years ago by • 0
1
vote
6
replies
1.9k
views
Redundancy reduction of de novo transcriptome assemblies with Compacta?
de-novo transcriptome redundancy-reduction
4.4 years ago by Dunois ★ 2.9k
0
votes
5
replies
1.9k
views
Cellranger count.srun issues
cellranger srun
updated 4.4 years ago by 153k • written 4.4 years ago by • 0
2
votes
2
replies
2.7k
views
Up-to-date GWAS Power Calculator and GWAS power comparison
GWAS power
4.4 years ago by moxu ▴ 510
1
vote
1
reply
3.6k
views
How to design WGCNA: one analysis over all sample or seperate analysis (using consensus module analysis)?
WGCNA RNA-seq
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 20
3
votes
2
replies
1.6k
views
Contradiction in Harzard ratio and Log fold change
LogFC Fold-change Cancer Hazard-Ratio HR
updated 2.0 years ago by 45k • written 4.4 years ago by ▴ 30
0
votes
0
replies
706
views
Refs/tools for protein interactomes
Protein PSI-MI Interactome Orthologs PPI
4.4 years ago by ian.will ▴ 30
0
votes
4
replies
1.5k
views
How to plot a image like this.
Genome R plot Cancer
updated 4.2 years ago by 45k • written 4.4 years ago by ▴ 50
0
votes
1
reply
867
views
How to get Data from https://www.orthodb.org/ by the list of UniprotID
orthoDB
updated 4.2 years ago by 45k • written 4.4 years ago by ▴ 10
121,896 results • Page 670 of 2438
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Answer: TCGA -derived Large RangeSummarizeExperient file
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
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Answer: Transfer harmony-integrated scRNA-seq data to scanpy by Madiha ▴ 10
Hi, I am not sure if you still remmeber the solution you followed that time. But I am stuck with similar problem. scVI is not working good …
Comment: Pipeline for downloading, aligning, and curating influenza A and B sequences for by GenoMax 153k
Have you looked at https://nextstrain.org/ and specifically https://github.com/nextstrain/seasonal-flu Software is available to do the ana…
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…
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