High Throughput Sequencing of Stable Isotope Probing Data
Analysis
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘HTSSIP’ version 1.4.1
Help Pages
| HTSSIP-package | HTSSIP: analyzing high throughput sequence data from nucleotide stable isotope probing experiments |
| as.Num | conversion to numeric |
| BD_shift | Assessing the magnitude of BD shifts with 16S rRNA community data by calculating the beta diversity between unlabeled control and labeled treatment gradient fraction communities. |
| calc_atom_excess | Calculate atom fraction excess |
| calc_Gi | Calculate G+C from unlabeled buoyant density |
| calc_Mheavymax | Calculate the theoretical maximum molecular weight of fully-labeled DNA |
| data-physeq_rep3 | (Data) A simulated HTS-SIP dataset |
| data-physeq_rep3_qPCR | (Data) qPCR data associated with the physeq_rep3 HTS-SIP dataset |
| data-physeq_S2D1 | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1) |
| data-physeq_S2D1_l | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1) |
| data-physeq_S2D2 | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2) |
| data-physeq_S2D2_l | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2) |
| delta_BD | delta_BD calculation |
| DESeq2_l2fc | Calculating log2 fold change for HTS-SIP data. |
| evaluate_matches | Evaluate String Interpolation Matches |
| expr_param_extract | Extract all quoted values in the expression used for phyloseq subsetting. |
| extract_expressions | Extract Expression Objects from String Interpolation Matches |
| extract_formats | Extract String Interpolation Formats from Matched Placeholders |
| filter_l2fc | Filter l2fc table |
| format_metadata | Format phyloseq metadata for calculating BD range overlaps. |
| fraction_overlap | Calculate the BD range overlap of gradient fractions |
| get_treatment_params | Get parameters for subsetting the phyloseq dataset |
| gradient_sim | Simulate HTS-SIP communities for 1 density gradient |
| heavy_SIP | Heavy-SIP analysis |
| HRSIP | (MW-)HR-SIP analysis |
| HTSSIP | HTSSIP: analyzing high throughput sequence data from nucleotide stable isotope probing experiments |
| HTSSIP_sim | Simulate a HTS-SIP dataset |
| match_brace | Utility Function for Matching a Closing Brace |
| match_placeholders | Match Expression Placeholders for String Interpolation |
| max_BD_range | Adjusting BD range size if negative. |
| OTU_qPCR_trans | Transform OTU counts based on qPCR data |
| overlap_wmean_dist | Calculating weighted mean beta-diversities of overlapping gradient fractions. |
| parse_dist | Filtering out non-relevant distances in distance matrix |
| perc_overlap | Calculate the percent overlap between two ranges (x & y). |
| phyloseq2df | phyloseq data object conversion to data.frame |
| phyloseq2table | Phyloseq conversion to a ggplot-formatted table |
| phyloseq_list_ord_dfs | Converting ordination objects to data.frames |
| phyloseq_ord_plot | Plotting beta diversity ordination |
| phyloseq_subset | Make a list of phyloseq object subsets |
| physeq_format | Checking format of phyloseq object for HTSSIP compatibility |
| physeq_list_betaDiv | calculating beta diversity for a list of phyloseq objects |
| physeq_list_ord | calculating ordinations from a list of distance matrices |
| physeq_rep3 | (Data) A simulated HTS-SIP dataset |
| physeq_rep3_qPCR | (Data) qPCR data associated with the physeq_rep3 HTS-SIP dataset |
| physeq_S2D1 | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1) |
| physeq_S2D1_l | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1) |
| physeq_S2D2 | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2) |
| physeq_S2D2_l | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2) |
| qPCR_sim | Simulate qPCR values |
| qSIP_atom_excess | Calculate atom fraction excess using q-SIP method |
| qSIP_atom_excess_format | Reformat a phyloseq object of qSIP_atom_excess analysis |
| qSIP_bootstrap | Calculate bootstrap CI for atom fraction excess using q-SIP method |
| SIP_betaDiv_ord | Calculating & plotting beta diversity for a list of phyloseq objects |
| stringterpolate | String Interpolation |
| tss | Total sum scaling |