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1,000 results • Page 2 of 20
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0
votes
0
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116
views
Error selecting species in stringApp on Cytoscape
stringApp cytoscape error species string
5 days ago by Regan • 0
1
vote
3
replies
236
views
Ensembl Homology REST requests - possible to download whole database and query locally?
python REST homology biomart ensembl
updated 4 days ago by ★ 2.1k • written 5 days ago by ▴ 60
0
votes
1
reply
181
views
Microarray DEG analysis scatterplot
DEGs Microarray Visualisation
updated 4 days ago by ▴ 550 • written 5 days ago by ▴ 10
0
votes
0
replies
100
views
How can I convert plink (.bed, .fam and .bim) fileset to .pgen file format?
format pgan plink file .bed
5 days ago by Mahan ▴ 70
1
vote
2
replies
159
views
Detection of O6 Guanine methylation levels
Detection NGS O6 methods levels methylation assays experiments Guanine
5 days ago by Guruprasadh ▴ 20
0
votes
0
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91
views
TCR data from HCA and ImmuneCode
TCR
5 days ago by Mamta ▴ 500
1
vote
4
replies
178
views
Change of -t argument in featureCounts affecting annotation
rnaseq subread annotation featureCounts
5 days ago by Marco Pannone ▴ 490
0
votes
1
reply
135
views
Is my code using Seurat correctly?
R Seurat
updated 5 days ago by 37k • written 5 days ago by ▴ 30
0
votes
1
reply
110
views
Creating dominant and recessive models for burden test
test dominant variant burden model recessive association Rare
updated 5 days ago by 840 • written 5 days ago by ▴ 50
2
votes
6
replies
244
views
Batch effect correction with cell type enrichment analysis
batcheffect r limma RNA-seq
updated 1 day ago by 840 • written 5 days ago by ▴ 50
0
votes
1
reply
162
views
Depending on which counts number, the genes are overexpressed either up or down regulated in GSEA ?
gene GSEA geneset
updated 4 days ago by ▴ 550 • written 5 days ago by ▴ 90
0
votes
1
reply
136
views
Is there a setting in GSEA software to filter counts less than 10 before go for GSEA analysis?
GSEA
updated 5 days ago by 840 • written 5 days ago by ▴ 90
1
vote
2
replies
205
views
Is there a tutorial/ demo on single cell nuclei-seq analysis
cell seq single sNuc-seq nuclei-seq sn-RNA
4 days ago by Emily ▴ 30
2
votes
2
replies
188
views
Why the number of genes decreased after dds (DESeqDataSetFromMatrix)?
DESeq2 R dds
updated 5 days ago by 65k • written 5 days ago by ▴ 90
0
votes
0
replies
101
views
How to do go enrichment under a parent GO term and its child GO term
enrichment clusterProfiler GO R
5 days ago by Scabbards • 0
1
vote
0
replies
106
views
How to compare multiple groups with count data?
statistics
5 days ago by Camilo Andres ▴ 10
0
votes
2
replies
114
views
Asking for introduction of a database
motif interaction domain protein
5 days ago by mohamadzare6022 ▴ 10
0
votes
4
replies
175
views
High number of unmapped reads in STAR
read count alignement STAR genecount
1 hour ago by Negara • 0
0
votes
0
replies
74
views
GTEx long read data
gtex long read short
6 days ago by Seong • 0
0
votes
0
replies
67
views
Statistical test for genomic annotation by ChIPseeker
ChIPseeker statistics PeakAnnotation
6 days ago by arisarkar88 • 0
0
votes
0
replies
88
views
Visualization of RNA editing on a gene - What is the best way and tool/plot that can be used?
RNA tools plots editing
6 days ago by Aiswarya • 0
0
votes
5
replies
210
views
FastQ: quality string length is not equal to sequence length
star fastq starlong
updated 6 days ago by 121k • written 6 days ago by • 0
0
votes
1
reply
86
views
Non-model organism , CluserProfiler message "No gene can be mapped"
ORA organism non-model
updated 6 days ago by 2.8k • written 6 days ago by • 0
0
votes
1
reply
105
views
How to compare multiple protein sequences and obtain single point mutations and their positions
python biopython bioinformatics pandas alignment
updated 6 days ago by 20k • written 6 days ago by • 0
1
vote
4
replies
169
views
Salmon WARNING: Detected suspicious pair
Salmon STAR
updated 6 days ago by 121k • written 6 days ago by ▴ 20
0
votes
0
replies
65
views
qc3C software for testing Hi-C data
qc3C Hi-C
6 days ago by gubrins ▴ 260
0
votes
1
reply
84
views
How can we use CARD database directly without using it RGI model of github
CARD
updated 6 days ago by 149k • written 6 days ago by ▴ 20
0
votes
1
reply
124
views
for loop and sapply for assigning name
R
updated 6 days ago by 9.9k • written 7 days ago by • 0
0
votes
1
reply
159
views
variant analysis using Freebayes
calling freebayes false variant positives
updated 6 days ago by ▴ 170 • written 7 days ago by ▴ 210
0
votes
1
reply
138
views
Beta-matrix. Differential methylation analysis
r analysis methylation differential
updated 6 days ago by ▴ 920 • written 7 days ago by ▴ 20
0
votes
1
reply
167
views
Difference between (~group) and (~0+group) in design matrix edgeR
R edgeR expression differential
updated 6 days ago by ▴ 920 • written 7 days ago by ▴ 60
0
votes
2
replies
164
views
How to code phased vcf genotypes into numeric sequence
vcf genotypes sequence phased
6 days ago by caredevil • 0
0
votes
1
reply
124
views
How to improve this WGCNA analysis
microarray WGCNA
updated 6 days ago by 2.8k • written 7 days ago by ▴ 30
0
votes
0
replies
89
views
Phylogeny using Mash
Mash phylogeny
6 days ago by SushiRoll • 0
1
vote
2
replies
130
views
How to find distance between two genomic features (one 0-based, one 1-based)?
distances bedtools coordinates BLAST genomic
7 days ago by bioinfo2345 ▴ 40
0
votes
0
replies
76
views
Get KOs for certain pathways
Orthologs KEGG Pathway
7 days ago by raniai • 0
0
votes
0
replies
103
views
Counting gene vs exons in featureCounts
RNA-Seq subread annotation featureCounts
7 days ago by Meisam • 0
0
votes
0
replies
74
views
Interferome
gene interferome ontology interferons RNA-seq
7 days ago by sarah.laverty20 • 0
0
votes
0
replies
79
views
Mouse variation VCF
VCF
7 days ago by German.M.Demidov ★ 2.8k
1
vote
3
replies
231
views
What is the best way to pre-process RNA-Seq data?
RNA-Seq z-score Normalization
updated 7 days ago by 37k • written 7 days ago by ▴ 30
0
votes
0
replies
99
views
macs2 bdgpeakcall only gives a few peaks
peaks macs2 Chip-seq bdgpeakcall
7 days ago by baijiangshan9726 • 0
0
votes
0
replies
93
views
TCGA data clustering
M3C ConsensusClusterPlus
7 days ago by aUser ▴ 20
0
votes
0
replies
91
views
Low number of nCount_RNA in single-cell RNAseq clusters?
quality cluster seurat nCount_RNA
7 days ago by shuaizh117 ▴ 10
0
votes
0
replies
89
views
Psuedobulk analysis of single-cell RNAseq data for GO term enrichment of per each sample.
GO scRNAseq Term seurat single-cell KEGG
8 days ago by Noora ▴ 10
0
votes
1
reply
111
views
Smartpca using Eigensoft
smartpca
updated 8 days ago by 149k • written 8 days ago by • 0
0
votes
1
reply
99
views
Geneious can't find all the sequences it needs in the selected file.
bam sam geneious
updated 8 days ago by 10k • written 8 days ago by ▴ 20
0
votes
3
replies
177
views
Deeptools comparing heatmap zMin and zMax across different plotHeatmaps
deeptools2.0 deeptools
updated 8 days ago by ▴ 490 • written 8 days ago by ▴ 20
1
vote
1
reply
104
views
Analyzing protein sequences
workflow sequences analysis protein
updated 8 days ago by 149k • written 8 days ago by ▴ 10
1
vote
1
reply
124
views
Software to remove the contribution of a study in a meta-analysis
meta-analysis summary-statistics statistics
updated 7 days ago by ▴ 920 • written 8 days ago by ▴ 20
1
vote
2
replies
134
views
moving .txt file to desktop
.txt desktop move file to
updated 8 days ago by 1.8k • written 8 days ago by ▴ 10
1,000 results • Page 2 of 20
Recent Votes
Answer: Unaligned Reads From Bowtie2
Four NCBI workshops in October (BLAST, Primer-BLAST, Metagenome analysis, Structures in iCn3D)
A: PLINK vcf to binary files error: Unused command line option: --vcf
PLINK vcf to binary files error: Unused command line option: --vcf
Answer: Parsing a genebank file and tsv file - extracting and outputting specific data t
Four NCBI workshops in October (BLAST, Primer-BLAST, Metagenome analysis, Structures in iCn3D)
haplotype phasing in duos
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Answer: empty peaks count, ChIP-seq, filter Bam, bed, bigwig, threshold, false peaks by maverenia • 0
I quess the problem is that I don't see the weak peaks in bigwigs, but they are counted in bed files. I there some approach to get bigwigs …
Comment: High number of unmapped reads in STAR by Negara • 0
yes in both the chromosome names are in the same format as chr1, chr2, etc.
Comment: Unaligned Reads From Bowtie2 by tiziana • 0
thank you for your answer. sorry if mine is a stupid question, as i am quite new to this, what does it mean "what is expected based on libr…
Answer: empty peaks count, ChIP-seq, filter Bam, bed, bigwig, threshold, false peaks by maverenia • 0
For the MACS2 callpeak I use the following conditions: Set lower mfold bound - 5 Set upper mfold bound - 50 Band width for picking regio…
Answer: How to convert Ensemble Gene IDs to gene symbols or Entrez Gene IDs? by Laura Luebbert ▴ 240
gget info https://github.com/pachterlab/gget
Comment: Parsing a genebank file and tsv file - extracting and outputting specific data t by Zach G • 0
Thank you very much. This is helpful. Now I tried implementing the code and it did give me a NameError: name 'category' not defined referri…
Comment: For loop rna sequencing alignment by iraun 4.7k
`404: Error Not Found` (Now seriously, you forgot to copy the error ;) ) So far the only thing that I can see is that the `done` in the e…
Answer: Why 6mA data are always 41 bps long? by acvill ▴ 160
The paper you reference ([Chen *et al*. 2019](https://doi.org/10.1093/bioinformatics/btz015)) includes the following excerpt, emphasis mine…
Answer: DEXseq estimateDispersions() returns error `replacement has 1 row, data has 0` by tien ▴ 10
I know the reason now. DESeqDataSet will automatically calculate count of other bins and generat column sample in colData. Previously, I ma…
Comment: For loop rna sequencing alignment by Pierre Lindenbaum 149k
not an answer but : you'd better use a workflow manager like snakemake or nextflow. > ..I am getting this error what is "this error" ?
Answer: Mapping PDB ID + chain ID to UniProt ID by Wayne ★ 1.4k
### Issue with pypdb route The pypdb route fails because the API pypdb access changed that it uses so that [the information no longer incl…
Comment: Parsing a genebank file and tsv file - extracting and outputting specific data t by Andrzej Zielezinski 11k
Thanks - now I understood. Please see my answer.
Answer: Parsing a genebank file and tsv file - extracting and outputting specific data t by Andrzej Zielezinski 11k
The following code produces the output you provided. Hope you find this code helpful. from Bio import SeqIO GBK_FILE = 'input…
Answer: Mapping PDB ID + chain ID to UniProt ID by Jiyao Wang ▴ 220
You can use an API from SIFT and parse the JSON output, e.g., https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/1kq2
Comment: Parsing a genebank file and tsv file - extracting and outputting specific data t by Zach G • 0
Great. So that is actually purposeful that there are no sequence ids common between the files. The idea is to add the sequence id's from bo…
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