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86 results • Page
2 of 2
Sort: Views
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Views
Votes
Replies
0
votes
1
reply
206
views
High amount of intronic/intergenic reads in SMARTer stranded total bulk RNAseq
RNA-seq
DNA
SMARTer
updated 4 days ago by
Ram
40k • written 4 days ago by
Mat
▴ 60
0
votes
1
reply
202
views
Esearch, Epost, and Efetch for Large Datasets in Biopython
eutils
biopython
entrez
updated 5 days ago by
Ram
40k • written 6 days ago by
Salem
• 0
0
votes
1
reply
200
views
how to calculate TM-score to p-value?
tmscore
pdb
protein
structure
updated 1 day ago by
kvcsnandi
• 0 • written 16 days ago by
Xylanaser
▴ 80
0
votes
1
reply
199
views
OMA in AWS cloud
OMA
AWS
updated 5 days ago by
Ram
40k • written 5 days ago by
Ksel
• 0
1
vote
1
reply
197
views
Read Counts from BAM file
bam
samtools
qualimap
readcount
updated 6 days ago by
ATpoint
76k • written 6 days ago by
Smriti
• 0
0
votes
1
reply
190
views
Identify parent of each read in a GAF
gaf
vgteam
vg
updated 6 days ago by
Jordan M Eizenga
▴ 360 • written 7 days ago by
cfourps
▴ 10
0
votes
1
reply
188
views
Merging the filename with tsv files for master file
genomics
updated 12 hours ago by
barslmn
★ 1.8k • written 2 days ago by
smrutimayipanda
▴ 20
0
votes
0
replies
180
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
5 days ago by
juliviglino
• 0
0
votes
0
replies
171
views
High pvalues when using clusterProfiler for seurat
clusterProfiler
4 days ago by
Ahmed
• 0
0
votes
0
replies
167
views
Current landscape of approaches to scRNA-seq with nanopore sequencers?
scRNA-seq
nanopore
single-cell
2 days ago by
LauferVA
3.7k
1
vote
5
replies
165
views
How the first sequencing template removed in pair end sequencing
NGS
RNA-seq
WGS
sequence
3 hours ago by
octpus616
▴ 80
0
votes
1
reply
163
views
Prank checkpoint and restore?
prank
alignment
updated 6 days ago by
Ram
40k • written 6 days ago by
Pit
• 0
0
votes
0
replies
163
views
scanpy problem for empty cells
scanpy
updated 4 days ago by
Ram
40k • written 5 days ago by
Andy
▴ 90
0
votes
0
replies
154
views
Compare peaks between clusters in sc-ATAC
Peak-Calling
Epigenome
scATAC-seq
updated 3 days ago by
Ram
40k • written 3 days ago by
Ahmed.waraky
▴ 10
0
votes
0
replies
151
views
Convert RNASeq V2 data in cBioPortal having RSEM normalized results to TPM values
bioinformatics
TPM
RNASeqV2
cbioportal
RSEM
updated 3 days ago by
4galaxy77
2.8k • written 3 days ago by
shakyaram079
• 0
3
votes
2
replies
150
views
Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
methylation
DMR
updated 13 hours ago by
Basti
★ 1.7k • written 1 day ago by
epianalysis
• 0
1
vote
5
replies
148
views
bcftools error merging two VCFs: REF prefixes differ
bcftools
VCF
1 hour ago by
Shane
• 0
0
votes
1
reply
144
views
RSEM not giving .genes.results and isoforms.results ; Plase check if you provide correct parameters/options for the pipeline!
genomics
transcriptome
rsem
ngs
updated 5 hours ago by
biofalconch
▴ 980 • written 11 hours ago by
kat.bi
• 0
0
votes
2
replies
140
views
how to create a loop in R
R
offtopic
updated 5 hours ago by
Ram
40k • written 12 hours ago by
mthm
▴ 50
1
vote
2
replies
138
views
Is it normal if regress out the cell cycle effects but the DEGs are quite the similar (no big changes)
regress_out
Cell_cycle
Seurat
1 day ago by
alwayshope
▴ 30
0
votes
0
replies
137
views
My rMATS output file is not showing gene symbols and only XLOC gene ID are being shown.
rMATS
rMATS-turbo
3 days ago by
Nipan
• 0
0
votes
3
replies
120
views
Running Rockhopper from a command-line
rockhopper
java
updated 5 hours ago by
Ram
40k • written 10 hours ago by
langziv
▴ 50
0
votes
1
reply
118
views
GO analysis after DESeq2
GO
updated 22 hours ago by
Ram
40k • written 23 hours ago by
oduduabasi.isaiah
• 0
0
votes
0
replies
117
views
Any way to predict hormone biosynthesis pathways in understudied organisms?
genomics
orthologs
biosynthesis-pathway
updated 6 days ago by
Ram
40k • written 6 days ago by
Mark
• 0
0
votes
1
reply
112
views
Download an example of fully-imputed VCF files ?
VCF
impute
updated 12 hours ago by
barslmn
★ 1.8k • written 1 day ago by
Ben
• 0
0
votes
1
reply
112
views
How to determine the total count for each gene in lymphotype B
scRNAseq
Seurat
updated 1 day ago by
fracarb8
★ 1.2k • written 1 day ago by
dalibenam64
• 0
0
votes
0
replies
101
views
filtering variants in a Strelka2 VCF file based on AD and AF
Filter
VCF
1 day ago by
Bogdan
★ 1.4k
0
votes
1
reply
98
views
Running Ibex on both BCR chains?
BCR
ibex
single-cell
updated 1 day ago by
Ram
40k • written 1 day ago by
actinia94
• 0
0
votes
0
replies
89
views
Spike-in normalization in ATAC-Seq with DiffBind
ATAC-Seq
spike-in
DiffBind
1 day ago by
frueher
• 0
0
votes
0
replies
85
views
How to annotate BED for tissue expression?
BED
annotation
1 day ago by
Fabio_bie88
• 0
0
votes
1
reply
56
views
DESeq2 error - converting result object into dataframe
R
DESeq2
Shiny
updated 3 hours ago by
Ram
40k • written 4 hours ago by
shasabhi1
• 0
0
votes
1
reply
51
views
Calculating haplotype and nucleotide diversity with deep amplicon sequencing data
data
Population
with
genetic
HTS
updated 3 hours ago by
Ram
40k • written 4 hours ago by
deorugz
• 0
0
votes
0
replies
50
views
ptt and rnt files that were created from assembly rather than a genome
rockhopper
genbank
updated 5 hours ago by
Ram
40k • written 7 hours ago by
langziv
▴ 50
0
votes
0
replies
44
views
How to remove chimera from 16S Sanger contigs
sanger-sequencing
chimera
uchime
updated 5 hours ago by
Ram
40k • written 7 hours ago by
eimanpharmacist
▴ 20
0
votes
0
replies
40
views
Which function is best for pathway analysis?
pathway
5 hours ago by
Chris
▴ 180
0
votes
0
replies
21
views
Troubles launch IGV on Linux(Debian)
IGV
updated 1 hour ago by
Ram
40k • written 2 hours ago by
PoscaXVIII
• 0
86 results • Page
2 of 2
Recent Votes
Comment: Filtering VCF to divide with equal sizes
Answer: How to plot proportion of cells in each cluster with scanpy?
Comment: How the first sequencing product removed in pair end sequencing
Comment: WGCNA Labeled Heatmap
C: Can I manually add nCount_RNA & nFeature_RNA to a converted Seurat object?
Comment: Hisat2 index and alignment question
A: Finding overlaps between GRanges objects
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Recent Replies
Comment: Violin plot (Monocle 3) - Troubleshooting
by
seattlescientist_01
• 0
I see the error message but I'm confused on what it's telling me.
Answer: Bacterial Pangenome Analysis
by
liorglic
★ 1.2k
I am not sure I understand why you think there is a problem with your analysis. It makes perfect sense that different blastp cutoffs produc…
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴ 110
Thank you for replying again. The "type" still causes issues but the reply by Radu Tanasa worked.
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴ 110
Thank you so much. That worked perfectly and it was much faster than what I was trying.
Answer: How to plot proportion of cells in each cluster with scanpy?
by
Radu Tanasa
▴ 60
Hi. If I get this right, you simply need to compute the percentage of cells in each cluster at the dataset level? ```py import pandas as p…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
ATpoint
76k
Why would that be an advantage?
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bk11
★ 1.2k
The following code will write percentage in your stacked barplot. cross_tab = pd.crosstab(adata.obs['leiden_0.6'],adata.obs['typ…
Comment: How to check RNAseq support for annotated genes?
by
BioinfoBee
• 0
@juke34 Thanks for the suggestion. I wonder if bedtool coverage or intersect can be used to check the transcript support or coverage for ea…
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴ 110
Because that was the code from the link. It is how they specified they had 2 groups of samples but I don't have 2 groups. Sorry for the con…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
bk11
★ 1.2k
No there is no bug in this. Please see carefully what the `error` message tells to you.
Comment: How to check RNAseq support for annotated genes?
by
BioinfoBee
• 0
@michaeld Thanks. I tried it using STAR to map the transcript to the annotation gtf file, and was planning to use featureCounts/gene Counts…
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bk11
★ 1.2k
Why you had `type` in your code above then?
Comment: Comparing multiple columns from two files using AWK
by
Ram
40k
R's dplyr will serve well here. ```r fileA %>% mutate(V3 = sub(V3, "chr","") %>% inner_join(fileB, join_by(V3 == chr, window_end <= V4, ..…
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴ 110
Thank you for the suggestion. Unfortunately, that does not work for me because I do not have a "type" argument in the adata.obs. I think th…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
seattlescientist_01
• 0
I'm still seeing errors: First I tried the code you mentioned except I use `clusters` instead of `embryo.time.bin` since this is a column…
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